In my case, I re-ripped a bunch of CDs and upgraded purchases from Beatport to AIFF. Once I got them, I converted them all to FLAC and imported them from a separate drive, much like yourself. In my case, I had a ton of ratings in iTunes, so I exported playlists of 1 star, 2 stars, 3 stars, etc. and imported each one. At that point, I selected all the affected MP3s and applied the new rating since I imported those as well (I have a lot of MP3s that I can't get in FLAC right now, but I'm sourcing new media to replace old stuff). I then made a new smartlist to help me carry over the MP3 ratings to the FLACs, and will phase out the old MP3s in favor of the new FLACs where possible.
[Media Type]=[Audio] [File Type]=[flac],[mp3] -playlistid==501829914 ~dup=[artist],[name] ~sort=[Name],[Artist]
The -playlistid==501829914 part means "don't use any tracks in the unrated MP3 playlist" so I don't waste my time dealing with them. I'm at the point where I'm starting to replace various MP3s with their FLAC equivalents, which is why I found this post interesting.
As for renaming an MP3 to a FLAC, that's just not going to work. The MP3 file is a stream, while the FLAC is a container that can hold streams. What you're doing is akin to renaming an MPEG-4 M4V video file to MP3 and trying to get it to play in a basic MP3 player. Not going to happen. And since the MP3s are already lossy, they're the result of a "tuned" process that rolls off "unnecessary" frequencies and uses a much lower effective bitrate per second, so all you'd be doing is "inflating" them to whatever FLAC compression level you're setting and at best, hoping for a file that sounds as good as the original MP3 did, much less the source material.