looking at your pictures, you might be right in that it is clear coated. it looks like it has metallics, and metallics usually are clear coated.
hmmm, pad selection. hard to say what is best for you.
when i was doing my stang, i found the CMA cutting pad with Meg's #80 Speed Glaze to be too much for the paint, and created more marring. the polishing pad and MPPC worked the best.
can you afford more than 3 pads? if so, get 1 cutting pad, 2 polishing pads, and 1 finishing pad. if not, just get 1 cutting pad, and 2 polishing pads. sorry i don't include the colors because for each manufacturer (Meg's and CMA) the color schemes are different. i've found the finishing pad to be nice and easy in applying NXT. it applies it thinly and evenly, not to mention you don't have to use as much of NXT to cover the whole car and it is much quicker than by hand. but if you can't afford it, you can still apply NXT by hand.
your steps sounds good: MPPC, #9, Color X or DACP with a polishing pad. A cutting pad might be really good on the roof though won't do nothing for the rust.

and be careful the pad doesn't pick up any rust and scratches the rest of the car! i think a polishing pad will work well for the rest of the car. just to warn you, you might have to make two or three passes to clean up the paint.
SMR - er, i think MPPC, #9, ColorX or DACP would be a SMR.

i think with most of the above products, you can go right to the NXT. just make sure all swirls and oxidization is gone before applying NXT.
you'll probably have to experiment with what pad and product will do the best job on your paint. and remember, use the least aggressive product and pad! i think that would be, from least to most aggressive, ColorX, #9, MPPC, DACP. i know DACP is the most aggressive, but it has been used (by others) with a polishing pad to get some good results.
with the NXT, do two coats, if possible, 12 hours between coats. if 12 hours is not possible, at least 1 hour between coats.
and thanks! it took me months of research to figure out the proper way of dropping my stang.

but that don't sound too good. do you know what kind of springs and struts/shocks you have?
and it's great to see a Fox Stang here. and detailing can be confusing, just ask if you have any more questions!