btw.. what's wrong with Silicone II?
You are about to find out...
... Anyone have any good suggestions of the best ways to remove the layers of silicone and similar caulks in all of the roof joints?
My opinion: Silicone is a great gasket material for parts that expand/contract at the same rate. It sucks as a caulk for anything that you ever think you might have to recaulk in your lifetime. (of course, there are places where it must be used, like fishtanks.) Nothing sticks to cured silicone. Not even silicone. And this includes the imperceptible film stuck to the surface where silicone was used. You have to remove it all to effectively recaulk. I hate that job, so I hate silicone.
Use some kind of urathane or latex RV caulk. Geocell MHRV2300 is one caulk that comes up often in camper forums. What I noticed about this one is that you can recaulk it to itself. Dicor is also a name I've seen. I would consider 3M 5200 which you can get at Lowes. Apparently it is very tough.
I just redid mine. The previous owner used silicone. I may have a slanted opinion.
I used eternabond so that I won't ever have to caulk again. (2inch white)
[Oops, forgot about the removal question]
If it is silicone - I tried some sort of silicone caulk remover that I bought at Ace Hardware. It didn't improve things over the elbow grease, putty knife, scratchy pads, rags, elbow grease, and elbow grease. In the non-silicone areas it was a matter of a quick flick of a utility knife, mineral spirits wipe down and it's ready to recaulk. You could use MEK or goof-off or goo-gone here as well.