I am not sure I can help you out with this. I have upgraded my DNN to 5.2.1 and do not have any display problems like that.

Instead of using the YAF profile provider, try using the ASPNet profile provider. You will still have to Inherit the YAF.Classes.Utils.YafUserProfile.

Yes it is possible. First thing to ask is if you were logged into DotNetNuke as the Host user.
If you were and added the second forum this way, You will only get the original forum.
If you log in as the Admin user for that particutlar DNN portal you wanted the second forum for, then adding the forum module to a page will result in a new forum being created.
Otherwize you will have to create a new board from the forum's admin menus.
Then select "Configure YAF Settings" from the MODULE drop down menu, and select the forum to view from there.
The Configue YAF Settings menu function is only available to the HOST user.

You do not need to install YAF as stand alone. The module includes all of the YAF files which are identical to a stand alone.
PA stands for Private Assembly. Older versions of DNN used to call modules (which are now called extensions) this.

This is due to the bug in DotNetNukeUrlBuilder.cs
See this post

I may be wrong but I believe YAF will check the db version against it's own version and if they are different it will redirect itself to the /install/default.aspx.

Normally if I upgrade or install YAF I run the install/default.aspx before I go to the forum.

As for the TODO comment, It may just be an old comment.

Removing the profile and role providers would have no impact to dnn.
The rest of the removal are all yaf specific.

It turned out I had trust set to full instead of high.

After testing the last release of the Dnn module, I found a few problems.

1. CookComputing dll was missing.
2. Web.config file was missing the role and profile provider sections.
3. Web.config file was missing the system.net section (defines email server).
4. DotNetNukeModuleEdit threw an error.
5. DotNetNukeUrlBuilder had an error.
6. Installing database would fail if trust was not set to "high".
7. Module install would fail if there were no CodeSubdirectories defined.

I recompiled the entire project to make sure all the assemblies were up to date, modified the yaf_dnn.dnn , modified the releasenotes.html,
modifed COPYING to an html format, corrected the bug in DotNetUrlBuilder.cs

Instead of just pointing out the errors I thought it would be easier to post the entire module here.

I found a way to add the providers in the dnn manifest file.
I am getting some stupid errors about not being able to write to the appsettings section to save the config password (now you know why I bang my head )
I'm working on it though.