nick, welcome to the d-word. sounds like you and your co-director have an interesting piece. it also sounds like you are in a similar position to many first-time filmmakers – lots of good footage, but not much knowledge about what comes next (other than a lot of editing). the d-word is definitely the right place for you to start learning...
i'll tackle a few of your questions, and let some others handle the rest:
1) regarding the shooting format differential, there's a really great (and inexpensive) piece of software called Nattress which does an awesome job of converting 29.97 footage to 23.98, which is what you want to edit in. for only $100, you get really great looking footage.
2) regarding Fair Use, you don't have anything to worry about regarding pop songs playing in the background of a cafe. as long as you don't use the pop songs in any "creative" way to enhance your scene(s), you are absolutely covered here. no need to buy licenses for the use of such music.
3) i think you have a good estimate for what it will take to finish the film, but you should really budget closer to 9 months of editing than just 6. things ALWAYS take longer than you think. normally, i would actually budget for about a year of editing with that much footage, but since your story is pretty chronological, that removes some of the storytelling hurdles.
4) you didn't mention the extra expenses of color correction, audio mix, and music score. i assume you already know about them, but those will all be fairly expensive items at the end of the game. Color correction averages around $10-12k, audio mix about $8-12k, and original music about $10-15k. and those are the low-to-mid-range estimates. it can be much more expensive depending on whom you use.
anyways, good luck, and feel free to post more questions. you'll get more responses if you just post one query at a time...