Tanks have about 20-30 gallons about 3 months old, 20-30 gallons fresh in the last week, and maybe 20 gallons old fuel from when I bought the boat in June.

have you removed the dist caps yet? had a set that ran bad after sitting a few months and when I opened the distributors they were rusted up bad and the springs had fallen apart. put in new distributors and crane boxes with the dist locked and the crane box controlling the timing and they have been flawless since.

Was anything removed from the engines or were they pulled 100% complete??
Why mess with the timing?? They should have been timed when they were removed.

First thing I would do is pull fuel filters and dump them into glass containers and check for water contamination.

I removed the caps and rotors, they appear to have been new from when the engines were built, which means only 35 hours of runtime but a few years old. Nothing obviously wrong with them on visual inspection. No visible rust on the distributors advance mechanisms. I sent the msd boxes in to be checked and they said all was well with them.

Prior to pulling the motors, i had an issue where the starboard motor would only deliver about 4300 rpm while the Port was still pulling to 4800 and more. Also running hot. So, timing seemed like a possible reason. Unfortunately I did not check the timing prior to messing with it.

I'll check the filters this week and report back.

Prior to pulling the engines I removed caps, rotors, carbs, plugs/wires, and headers.

I messed with the timing because of a discrepancy in the way the 2 engines were running, both in power and water temp.

I just pulled fuel filters and dumped them into a glass pitcher. Few bits of grit but no obvious water or other visible contamination. I'll let the pitcher sit to see if anything settles out but not looking like massive water contamination.

many things, some setups really need a lot of base timing, many run dist locked to help idle, I personally have 0 faith in MSD(may soon die) parts, boxes fail when they feel like it, magnectic pickups in Dist fail as well(chinese made) Next need a wideband to tune carbs correctly, without it you are pissing in the wind. As far as dist are concerned the DUI's are one of the best out there if you have room for the large cap HEI.

what was the reason for this

To minimize the chance for breakage when pulling the motors out.

are these standard firing order cams ?