You may need to remove long lengths of trim or some siding to repair damaged frame work. It's not a bad thing, it's just another area that you can improve (at least that's what I told myself).
I have an aluminum roof that had roofing tar, silicone caulk, acrylic caulk, spray sealers, and some of the original mortite type of tape (now called butyl tape). I used a variety of mechanical removal tools like scrapers, putty knives, etc. I also used power tools like grinders with a wire brush. When I had everything scraped, using a heat gun and then wire brushed, I used solvents to remove the residue. You'll have to be careful with a rubber roof, don't use any petroleum chemicals. 3M makes an excellent caulk remover that should dissolve most caulks and sealants. The trick is to slather it on, cover with plastic wrap, and give it 12 hrs. to work.
