That's what I figured out after replying. I just PMd OmegaMattman to ask him what software he used for merging the two different crawls on his DVD set (not sure if it is Rebellion or Hyperspace), and I don't even know if the method he used applies to blu-rays. I don't remember any lag in his version, but I could be wrong, and I believe I left his sets at my mom's house, so I can't check myself.
As for the audio tracks I might only keep the tracks of the languages which have a preservation with their own crawl available plus the voice over english crawl tracks. I'm also thinking of a sub-menu option for every language with multiple audio tracks, but I'm not even sure it might be possible, either for any software or for Blu-ray players.
There will be drawbacks no matter what, i just want to make them as painless as possible.