Pics would help us try and figure out what the best approach would be. However lots of valid points have been brought up already. If the clear coat is thin you don't want to be attacking it with Surbuf pads. Regardless of how "safe" a PC is, you can still burn through thin clearcoat with ease. Also, you might not really need the Surbuf pads. They are as aggressive as you can get on a PC, so they really aren't the best place to start. And a final note on the surbufs, you really shouldn't be doing a one step or finishing with them. I know people do, but IME they ALWAYS leave some sort of micromarring, whether it be faint swirls or little hash marks in the paint. IMO you should ALWAYS follow a surbuf pad with a softer foam pad and a finishing polish.
All that being said depending on the state of the clear coat and how hard it is, you might be able to get great results using just foam pads. I would say to get a couple LC orange pads and a couple LC white pads. The orange pads coupled with a compound (M105, Meguiars Ultimate Compound, OPT Compound) should be able to remove the bulk of your defects without taking off too much clearcoat. Then you can follow that up with the white pads coupled with a refining polish (M205, Menzerna 106fa). This should leave you with a pretty much defect free finish that has a lot of gloss and shine.
Now, as far as the MF system goes, its MAJOR strength IMO is the fact that it's a kit and it's pretty much foolproof. It takes all the guess work out of what product to use with what pad. Now this does limit it in some ways, but it also is what makes it so easy to use. If your paint is OEM (very important) I don't see a reason not to give the MF system a try. The cutting pads aren't as aggressive as the Surbuf pads, so you shouldn't have to worry as much about thin clear. Also they GENERALLY finish down better than the Surbuf pads. I've used them on some very soft paint and they left quite a bit of haze, but on most cars I've used them on they leave a very nice finish. then you can just follow it up with the finishing pad and polish and you're good to go.
Hope that helps.