The biggest issue, after replacing rotten roof sheathing and structure is always roof "penetrations". If these are not done PERFECTLY, you have just started the cycle over again.
I am not a fan of EPDM and lap sealants. IMHO, they will all fail (leak). TPO uses heat "welded" seams. If done correctly the 2 pieces have become one.
Replaced my EPDM roof with material supplied by Dicor. Had no leaks so no roof repair as in wood was needed. Did put luan over the existing plywood roof so would have better adhesion. Had 2 good helpers, it went about like you would expect. Remove old material and replace. No problem with ac and vents etc. Just do it.