1) I agree with Punkn--make sure to have a supplemental list for every advanced program. I had a few different supplemental lists, depending on the advanced program. But I ranked every prelim program in every supplemental list--it's just the order that differed.
As far as where to apply, personally I didn't have the time/money to have 3-4 prelims per geographical area of each of my advanced programs. So, I only applied to three main categories of programs:
1) Prelim-medicine and TY's within the same metropolitan area (Chicago) as my medical school. Lots of prelims and no cost except gas to get to them. Saves me time & money. It would've been very easy to just stay where I was for one more year (3-4 programs were a very short 5-15 min commute away)
2) Prelim programs that were linked and/or interviewed on the same day as the advanced program. MCW, VCU, and Mayo I think were the only ones that did one or the other (of the places I interviewed--I'm sure there are many others). Other programs had categorical programs (that would make life easy...)
3) TY programs that were a good balance of education/elective time (I didn't want a cush program--why waste the year?) that were within a half-day's drive (basically one state in any direction). In my mind, it still wasn't worth flying out just for a TY interview.
I saw no reason to apply to separate prelim programs in, say, California, or the east coast, etc. I wasn't going to fly out there just for a prelim interview. I interviewed at 13 PM&R programs and 8 prelim/TY programs, and I was tired by the end (but it was still a blast). And Nov was an easy month and I had Dec off. So plan your interviews strategically--in January, you will start getting worn out. (So I scheduled most of the prelims I was less interested in at that time...)
2) I think TY's are worth applying to, if you apply to ones worth going to. Most of the ones in the big and desirable cities will be a long shot unless your board scores are stellar. And, in my (n=1) experience, those seem to be the really cush programs, and in my opinion, also happen to be the less educational programs. I liked the elective time a TY offered, but it's important to know your medicine, especially if you're interested in inpatient rehab--so I'd look into TY's that you think will adequately prepare you. I think that if the residents (at any program) brag about all the free time they have, you should probably consider ranking that program low or not at all.
3) I'd recommend using the same personal statement--everyone does. Or at least almost everyone seems to. I sure didn't change mine one bit, and no program expected me to change it. I'd actually guess that more programs would want to know why you want to go into your chosen field than into a pre-lim year (everyone would just write the same thing about how it would prepare them for "x" specialty).
Best of luck with your application, and best of luck on your away rotations!