When you get the structure back in good shape and the metal skins back on then is the to install windows....doors....roof jacks and fixtures. Simply reinstall them like OEM which is butyl tape first. I use a wooden tongue depressor or plastic putty knife and remove the excess squeezed out. Then is the time to Use a self leveling sealant over the screws and where the butyl squeezed out.
Same butyl tape under the windows and doors flanges just like the everything on the roof. Using a sealant on a vertical surface is optional.
My '97 31' 5th wheel trailer windows and doors have no secondary sealant ...just the butyl tape. No leaks....but I do my usual yearly check on everything.
Most aluminum roofing in that era was seamless by then. If so and your adding a coat be sure and use white.
I did this type work part time on mobilehomes and rvs back in the '60s and '70s. Todays sealants are amazing compared to tar and caulking that got rock hard back then.