The latest versions of the FS2 and FRED2 executables are available on
this forum. Check the "CVS Builds" sticky thread at the top for the very latest files. Unfortunately, threads from the past few days or so have gone to Sector 14 (they've vanished) so if you're looking for a build posted that recently you may have to do a little link hunting. I myself generally don't download the very latest versions as they come out so someone else will have to tell you which are stable and up to running TBP, assuming you don't figure out through your own experimentation.
I can't think of what would be limiting you to only placing two wings in FRED2. Can you post what kind of error message you're getting, if any?
As for the wave files, if you're referring to the voice overs from vanilla FreeSpace 2 then those are kept in a .vp file that is installed with FS2 and doesn't come with TBP. The Babylon Project comes with its own wingman personas and default message sound files instead. If you want to use one of FreeSpace 2's voice files in your mission you can always extract it from the appropriate .vp file with VPView and put it in the data/voice/special directory of your TBP folder.
Like 0rph3u5 said, TBP comes with its own comm animations to replace the ones used in FS2 and these have different filenames. If the Search function was working I could dredge up the old filename-image list, but it's not.