you are set up correctly wiring wise. I don’t have an issue using a cheap walmart MaXX 29g for my trolling motor batteries because if they fail, there’s a walmart almost everywhere where I can get them replaced. I do however never go cheap on the cranking battery as it runs all my pumps, motor, electronics, etc. You want something with the most reserve you can afford. I like something 200+ reserve. You don’t make long runs it sounds like so the more reserve you can find in a cranking battery in your budget, the better. Just make sure it has enough CCA/MCA to start your motor. I don’t know the specifics of a 90h merc but I can’t imagine the requirements are too high. I
You should be charging your batteries directly after you get off the water. You are running them down low, letting them sit for what sounds like a few weeks at a time, and then charging them. You’re killing the batteries.
You’re having cranking battery issues because your motor isn’t charging the battery. A few mile run generally isn’t enough to fully charge a cranking battery. Yours don’t seem to be holding a charge for the reason I stated above. However…it doesn’t sound like your rectifier/ regulator is working anyway. Your engine should be charging your cranking battery after 1500 rpms(ish) to WOT. You should see a voltage of 14.5 give or take when cruising and then, assuming it’s charged and your battery is good, a reading of 12.6 at rest. You aren’t seeing anything. That’s bad. Even if it was working it doesn’t sound like your batteries are holding a charge anyway. I’m guessing you need 2 new batteries and a, hopefully, just a new rectifier that is very simple replacement. Hopefully it isn’t a combination of the stator, rectifier, voltage regulator, etc.