It looks like you are doing a great job with your project, unfortunately you will still have a rubber roof. I had rubber roof membrane failure after 5.5 years service. Moisture was leaking "through" the membrane not the more common caulking leaks. I full time and constant worry about roof issues was eating me up and after the membrane failure was discovered I made a decision.
It wasn't cheap, but then a new RV after a leak that wasn't found in time isn't cheap either and a new rubber roof made no sense to me. So my solution was
RV Flex Armor.
My interior is quieter due to the thickness of the new roof and a lifetime no leak guarantee. I sleep much better now and zero caulking that will fail and zero rubber roof that has failed.
Ed
KM4STL
2006 GMC 2500HD CCSB 4x4 Duramax/Allison, Titan 52 gallon fuel tank, Prodigy Controller, B&W Companion Hitch, Progressive Industries EMS-PT50C, TST Systems 507 TPMS
2010 Jayco Designer 35RLTS,Cummins/Onan RV QG 5500 EVAP
Fulltime since 2010