The question is what would be the solution to have the old posts and their adjacent category urls displayed correctly as I've described above?
Comments on your .htaccess code first:
Most of the Apache core code should be (and probably is already) in the httpd.conf file. You're wasting resources repeating the read/parse/execute of each of these directives MULTIPLE times for each file request made of the server.
You are wasting resources asking Apache to check whether various modules exist MULTIPLE times for each file request made of the server. I have a standard (i.e., do NOT take it personally) rant for the MULTIPLE mod_rewrite checks:
[rant #4][indent]The definition of an idiot is someone who repeatedly does the same thing expecting a different result. Asking Apache to confirm the existence of ANY module with an <IfModule> ... </IfModule> wrapper is the same thing in the webmaster world. DON'T BE AN IDIOT! If you don't know whether a module is enabled, run the test ONCE then REMOVE the wrapper as it is EXTREMELY wasteful of Apache's resources (and should NEVER be allowed on a shared server).[/indent][/rant 4]
You DO have code in your pre-WP section which redirects to an _index.php file - look to that (use your LOG file to examine redirection handling) for your _index.php problem.
The long stream of mod_alias directives will be processed before mod_rewrite (because mod_alias is a core directive and mod_rewrite is not - it must be specifically enabled). This is another massive waste of resources (it belongs in your httpd.conf or httpd-vhosts.conf file, not in .htaccess) and you can use mod_rewrite's regex capability to match patterns and redirect accordingly.
I don't know how you got to such a point with your .htaccess file but I would seriously recommend a major clean-up. That would also allow you to find problems within your code much easier.
As for your desire to display two types of URIs, I don't believe that WP can function that way (ergo, I try to keep away from WP and other CMS's). Using mod_rewrite, you CAN create new URI formats and redirect TO the new format(s) while serving the original (functional) format. WP does a little of that for you but I think you're asking for more than WP can do (natively - is there a plug-in you're using?).