Tied it all together, very rough working version of the setup is in place now.

src/com/fsck/k9/activity/setup/AbstractSetupConfirmActivity.java

@@ -12,14 +12,12 @@ package com.fsck.k9.activity.setup;
         'browse' through the available hosts. This consists of 2 auto hidden/unhidden buttons and the necessary callbacks.
         The need for this is questionable, if the devs/community decide for, I'll finish the code, if not it will be removed.
  */
-import android.content.Context;
+
-import android.content.Intent;
 import android.os.Bundle;
 import android.text.Editable;
 import android.text.Html;
 import android.text.TextWatcher;
 import android.text.method.LinkMovementMethod;
-import android.text.method.MovementMethod;
 import android.view.View;
 import android.widget.*;
 import android.widget.AdapterView.OnItemSelectedListener;
@@ -38,29 +36,14 @@ import java.util.List;
 
 public abstract class AbstractSetupConfirmActivity extends K9Activity implements View.OnClickListener, OnItemSelectedListener {
 
-    private static final String EXTRA_ACCOUNT = "account";
+    protected static final String EXTRA_ACCOUNT = "account";
-    private static final String EXTRA_CONFIG_INFO = "configInfo";
+    protected static final String EXTRA_CONFIG_INFO = "configInfo";
-    private static final String EXTRA_EMAIL = "email";
+    protected static final String EXTRA_EMAIL = "email";
-    private static final String EXTRA_PASSWORD = "password";
+    protected static final String EXTRA_PASSWORD = "password";
 
     private final String LOCALPART_EMAIL = "%EMAILLOCALPART%";
     private final String WHOLE_EMAIL = "%EMAILADDRESS%";
 
-    public static void actionConfirmIncoming(Context context, Account account, AutoconfigInfo info) {
-        Intent i = new Intent(context, AccountSetupConfirmIncoming.class);
-        i.putExtra(EXTRA_ACCOUNT, account.getUuid());
-        i.putExtra(EXTRA_CONFIG_INFO, info);
-        context.startActivity(i);
-    }
-
-    public static void actionConfirmIncoming(Context context, String email, String password, AutoconfigInfo info){
-        Intent i = new Intent(context, AccountSetupConfirmIncoming.class);
-        i.putExtra(EXTRA_EMAIL, email);
-        i.putExtra(EXTRA_PASSWORD, password);
-        i.putExtra(EXTRA_CONFIG_INFO, info);
-        context.startActivity(i);
-    }
-
     // data
     protected Account mAccount;
     protected AutoconfigInfo mConfigInfo;
@@ -116,7 +99,7 @@ public abstract class AbstractSetupConfirmActivity extends K9Activity implements
         mPassword = getIntent().getStringExtra(EXTRA_PASSWORD);
 
         String accountUuid = getIntent().getStringExtra(EXTRA_ACCOUNT);
-        if(accountUuid != null)
+        if(accountUuid != null && !accountUuid.isEmpty())
             mAccount = Preferences.getPreferences(this).getAccount(accountUuid);
         else mAccount = Account.getBlankAccount(this, mEmail, mPassword);
 
@@ -164,7 +147,6 @@ public abstract class AbstractSetupConfirmActivity extends K9Activity implements
         switch( view.getId() ){
             case R.id.confirm_ok_button:
                 finishAction();
-                finish();
                 break;
             case R.id.confirm_next_server_button:
                 // TODO: write this,... it will probably never be used since no isp has 2 host for exact the same thing

src/com/fsck/k9/activity/setup/AccountSetupAutoConfiguration.java

@@ -384,7 +384,7 @@ public class AccountSetupAutoConfiguration extends K9Activity implements View.On
             // launch confirm activities
             }else{
                 AccountSetupConfirmIncoming.actionConfirmIncoming
-                        (this, mEmailAddress, mPassword, mAutoConfigInfo);
+                        (this, null, mEmailAddress, mPassword, mAutoConfigInfo);
                 finish();
             }
             break;

src/com/fsck/k9/activity/setup/AccountSetupConfirmIncoming.java

@@ -6,7 +6,10 @@ package com.fsck.k9.activity.setup;
     the final settings.
  */
 
+import android.content.Context;
+import android.content.Intent;
 import android.util.Log;
+import com.fsck.k9.Account;
 import com.fsck.k9.K9;
 import com.fsck.k9.helper.configxmlparser.AutoconfigInfo;
 import com.fsck.k9.helper.configxmlparser.AutoconfigInfo.ServerType;
@@ -19,6 +22,19 @@ import java.net.URLEncoder;
 import java.util.List;
 
 public class AccountSetupConfirmIncoming extends AbstractSetupConfirmActivity {
+
+    // account is allowed to be null
+    public static void actionConfirmIncoming(Context context, Account account, String email, String password, AutoconfigInfo info) {
+        Intent i = new Intent(context, AccountSetupConfirmIncoming.class);
+        if( account != null )
+            i.putExtra(EXTRA_ACCOUNT, account.getUuid());
+        else i.putExtra(EXTRA_ACCOUNT, "");
+        i.putExtra(EXTRA_EMAIL, email);
+        i.putExtra(EXTRA_PASSWORD, password);
+        i.putExtra(EXTRA_CONFIG_INFO, info);
+        context.startActivity(i);
+    }
+
     @Override
     protected List<? extends AutoconfigInfo.Server> getServers() {
         return mConfigInfo.incomingServer;
@@ -42,7 +58,9 @@ public class AccountSetupConfirmIncoming extends AbstractSetupConfirmActivity {
                     mCurrentServer.hostname,
                     mCurrentServer.port,
                     null,null,null);
-            mAccount.setTransportUri(uri.toString());
+            mAccount.setStoreUri(uri.toString());
+
+            AccountSetupConfirmOutgoing.actionConfirmOutgoing(this, mAccount, mEmail, mPassword, mConfigInfo);
         }
         catch (UnsupportedEncodingException enc) {}
         catch (URISyntaxException use) {
@@ -51,5 +69,6 @@ public class AccountSetupConfirmIncoming extends AbstractSetupConfirmActivity {
             * convenience.
             */
         }
+        finish();
     }
 }

src/com/fsck/k9/activity/setup/AccountSetupConfirmOutgoing.java

@@ -6,11 +6,33 @@ package com.fsck.k9.activity.setup;
     the final settings.
  */
 
+import android.content.Context;
+import android.content.Intent;
+import android.util.Log;
+import com.fsck.k9.Account;
+import com.fsck.k9.K9;
+import com.fsck.k9.Preferences;
 import com.fsck.k9.helper.configxmlparser.AutoconfigInfo;
 import com.fsck.k9.helper.configxmlparser.AutoconfigInfo.ServerType;
+import com.fsck.k9.helper.configxmlparser.AutoconfigInfo.AuthenticationType;
+
+import java.io.UnsupportedEncodingException;
+import java.net.URI;
+import java.net.URLEncoder;
 import java.util.List;
 
 public class AccountSetupConfirmOutgoing extends AbstractSetupConfirmActivity{
+
+    // account is allowed to be null
+    public static void actionConfirmOutgoing(Context context, Account account, String email, String password, AutoconfigInfo info) {
+        Intent i = new Intent(context, AccountSetupConfirmOutgoing.class);
+        i.putExtra(EXTRA_ACCOUNT, account.getUuid());
+        i.putExtra(EXTRA_EMAIL, email);
+        i.putExtra(EXTRA_PASSWORD, password);
+        i.putExtra(EXTRA_CONFIG_INFO, info);
+        context.startActivity(i);
+    }
+
     @Override
     protected List<? extends AutoconfigInfo.Server> getServers() {
         return mConfigInfo.outgoingServer;
@@ -23,6 +45,53 @@ public class AccountSetupConfirmOutgoing extends AbstractSetupConfirmActivity{
 
     @Override
     protected void finishAction() {
-        //To change body of implemented methods use File | Settings | File Templates.
+        try {
+            String userInfo = null;
+
+            // check if authentication is required
+            if (mCurrentServer.authentication != AuthenticationType.none &&
+                mCurrentServer.authentication != AuthenticationType.clientIPaddress )
+            {
+                userInfo = URLEncoder.encode(mUsername, "UTF-8") + ":" +
+                           URLEncoder.encode(mPassword, "UTF-8") + ":" +
+                           mCurrentServer.authentication.getAuthString();
+            }
+
+            URI uri = new URI(
+                    getScheme(),
+                    userInfo,
+                    mCurrentServer.hostname,
+                    mCurrentServer.port,
+                    null,null,null);
+
+            mAccount.setTransportUri(uri.toString());
+            AccountSetupCheckSettings.actionCheckSettings(this, mAccount, true, true);
+
+        } catch (UnsupportedEncodingException enc) {
+            // This really shouldn't happen since the encoding is hardcoded to UTF-8
+            Log.e(K9.LOG_TAG, "Couldn't urlencode username or password.", enc);
+        } catch (Exception e) {
+            /*
+             * It's unrecoverable if we cannot create a URI from components that
+             * we validated to be safe.
+             */
+            // TODO: handle this
+            //failure(e);
+        }
+    }
+
+    @Override
+    public void onActivityResult(int requestCode, int resultCode, Intent data) {
+        if (resultCode == RESULT_OK) {
+            if (Intent.ACTION_EDIT.equals(getIntent().getAction())) {
+                mAccount.save(Preferences.getPreferences(this));
+                finish();
+            } else {
+                // have to pop up to ask if it should be default account now
+                // hard-coded now for test purposes
+                AccountSetupOptions.actionOptions(this, mAccount, true);
+                finish();
+            }
+        }
     }
 }

src/com/fsck/k9/activity/setup/AccountSetupIndex.java

@@ -186,6 +186,7 @@ public class AccountSetupIndex extends K9ListActivity implements OnItemClickList
 
     private void startSettingsDetection(String email, String password) {
         AccountSetupAutoConfiguration.actionAttemptConfiguration(this, email, password);
+        finish();
     }
 
     /*

src/com/fsck/k9/helper/configxmlparser/AutoconfigInfo.java

@@ -7,6 +7,9 @@
 
 package com.fsck.k9.helper.configxmlparser;
 
+import java.io.UnsupportedEncodingException;
+import java.security.PrivateKey;
+import java.security.PublicKey;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
@@ -52,7 +55,24 @@ public class AutoconfigInfo implements Parcelable {
     /*******************************************************************************
         Define types for some of the data
      *******************************************************************************/
-    public static enum AuthenticationType { plain, secure, NTLM, GSSAPI, clientIPaddress, TLSclientcert, none, UNSET };
+    public static enum AuthenticationType {
+        plain(1), secure(2), NTLM(-1), GSSAPI(-1), clientIPaddress(0), TLSclientcert(-1), none(0), UNSET(-1);
+        /*
+            K-9 only supports plain or CRAM-MD5 so we'll toss an error for all the rest and just check this manually
+         */
+        private int type;
+        AuthenticationType(int type){ this.type = type; }
+
+        public String getAuthString() throws UnsupportedEncodingException {
+            switch( type ){
+                case 0: return "";
+                case 1: return "PLAIN";
+                case 2: return "CRAM_MD5";
+                default: throw new UnsupportedEncodingException();
+            }
+        }
+    };
+
     public static enum SocketType { plain(""), SSL("ssl"), STARTTLS("tls"), UNSET("");
         private String schemeName;