Check that all connections are clean and tight with no corrosion and ground leads are the same. If it persists, then I'd consider the voltage regulator.
First - Shaft alignment should always be done with the boat in the water - And in the water for at least a week after being on the hard. Second - 8" and 2"? I think there was a miscommunication, or they had unbolted the engine mounts and moved the engine when the transmission was removed...
I am also a fitness enthusiast on a high protein diet and no issues with clogging the head at home or on the boat. I'd suggest either upgrading your head or check with your doctor for other potential remedies.
I made a similar change last summer with a 25hp Yamaha electric start / power trim and also have a swim platform davit system. I selected an AGM garden tractor battery and so gar its worked great. I think I have 330 CCA.
We have a Sonos system at home and are very happy with it. Until now, we've made do with various Bose bluetooth speakers but am thinking about moving to the Sonos Move 2 speakers but will likely skip the sub woofer. A little too much for use in the marina and waaay too much when anchored out.