We replaced a skylight several years ago when we owned a 5ver. Used new screws, put a strip of butyl tape under the edge, run a very small bead of caulk around the edge(probably optional) and finished by applying Eternabond. Would use it again in a heartbeat if/when needed on our MH. You can purchase the Eternabond here at IRV2 upgrades.
Go to the search box and type in Eternabond.http://www.rvupgradestore.com/
Eternabond and the butyl tape can also be purchased here along when a small roller to better seal the tape with.http://www.bestmaterials.com/roof_repair.aspx
Last but not least, it might be usefull to have this website available if you make a mistake
and have to remove the tape.How to remove Eternabond Tape