To answer your questions:
-The ONLY benefit to waiting for your MCAT results before you submit your app is that if you bombed the MCAT and don't want to continue the app process, then you simply don't submit the rest of your stuff. HOWEVER, the next time you apply you are going to have to put down all your MCAT scores anyways, so why bother. Waiting for your MCAT scores just delays the process in my opinion. I imagine that TMDSAS puts things in order and checks them off as they get them. So if they only lack your MCAT, then boom, it's ready to go once they get it. If you wait and submit every thing else in after the scores are released you may be at the back of the line. It doesn't hurt at all to submit your app early. SO, I WOULD SUBMIT EVERYTHING ASAP, regardless of MCAT scores.
-If you bomb the MCAT, which I did the first time. I had already sent in my app, checked the box that I would not be taking it in Aug., so on and so forth. I got my scores back, got angry, took a day off, then started hitting the books the next day. I made a simple phone call to TMDSAS, told them I am retaking the MCAT in August and wanted to know if they could change that for me on my app. They did so, without hesitation. It's as easy as that.
-Your last two questions can be answered together. Once you finish your app send it. Once you get your transcripts, send it. Hound your PredMed advisor to send your LORs asap. Not too much though. You don't want to piss her off. Try sucking up, you'll need the practice for later on down the road. There is no penalty for sending stuff in early. So why not. I did, and so did everyone else I know.
I know the TMDSAS website isn't the greatest, but a lot of people don't read before hand either. I always thought TMDSAS was very polite and easy to work with. Email them rather than call them unless you need to make changes to a submitted app. If you have more questions you can pm me. I have been in your spot before. Good luck.