Roof and Deck Leaks HELP

I am in California and have a house with a flat roof and a deck wrapping around the house. When I did a remodel I used a roofer that is long gone. He hot mopped around some air conditioning ducts that were installed and since I have had leaks around several of the ducts. Painting a water based liquified membrane around these flashings has solved some of the leaks but not all. I also have 1 fantom leak that starts leaking almost as soon as it starts raining. There are two roofs on the house, the last being done in about 1997. It is roll composition. Some roofers say re-roof and some say coat. Reroofing means removing and resetting all of the air conditoning ductwork which adds cost to the job. The roofers that recoat say coat with a polyurethance coating and the problem will be solved? Still others say use a monolithic shhet like durolast. Even the ones that re-roof can't agree. Some say torch, some say hot mop. I am so confused and winter is coming and the roofers in so cal are so busy that they can write their own ticket at this point. Not sure what to do.
Secondly, the same roofer did the deck. He did not tape the plywood joints prior to putting down a polyethlene sheet and rubber substance with aggregate. The joints opened up during last winter and leaked like a collander. Also a rear part of the deck which was framed over an existing redwood deck has some areas maybe 4" X 4" of dryrot that can be scooped out like powder. Needs patch repair but the whole deck system needs to be addressed. Is a aggegate and polyurethane coat better or should I go a fiberglass type system which is heavier? I understand that to do the fiberglass system they staple metal lath down, float the aggegate. It is heavier than the polyurethane but seems very impervious, but does it crack easier? Not sure what to do.
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