Replacing Skylight

[BradW]

I bought my Flagstaff slightly used and the previous owner painted the skylight, along with the roof vents with black spray. I can live with the vents like this, but I have ordered a new clear lexicon SL for the shower.
So I am looking for some direction on replacing this skylight.
Questions I have are,,,can I merely use caulk between the roof and the SL or is it a must to use butyl tape there? Next, I have a rubber roof, so what is recamended to clean off the old caulk after getting the majority with a putty knife? Is mineral spirits the answer here or something else?
Any other tips or suggestions would be appreciated as well.
Thanks

[Dave_Monica]

Here's a link to instructions from eHow... How to Replace an RV Skylight | eHow

Dave