great job,i wished i saw this earlier,,ive built boats and campers most of my life,youve got a water/wood rot problem, heres my recomendations,,1.use marine-grade plywood[its put together with waterproof epoxy/glue],2.everything wood should be coated epoxy fiberglass resin [most important to coat cut ends] this will stop the water intrusion,3.that butyl rubber [its used by builders because its cheap][most builders of campers/trailers/motorhomes use the cheapest parts around] your using is junk,everything should be sealed with a good quality silcone caulk [its flexes],most of your leaks are caused by holes [drilled/cut] into the camper by the manufacturer,the PO was just trying to fix things as best as he could[probably not a real handyman] 4.make sure you ck the other siding and roof [you are so far along ,it would'nt take much more to pull off the other windows and siding to caulk and seal the siding panels] 5.try to thru bolt everything[waste water,gen,propane,ladder [lag screws/deck screws,staples,nails]6.ck every pice of wire/cable,make sure there are gromats anywere wiring runs thru a hole[most manufactures cut every corner they can] and ck every electrical connection,,good luck ,your doing a great job and just keep asking for help-somebody will be happy to help,,,also dont take anything im saying as putting down your work,this is just what ive found by fixing wood rot for the past 25+ years