I just wanted to close the loop on this as several people helped me.
The problem was definitely fuel. Once the boat hit the water, I filled the tanks up with fresh gas. STBD took only 60 gallons to fill which meant I had 60 gallons of bad gas mixed with 60 gallons of good. I added about 12 OZ of StarTron to the tank as well on top of the 16 oz I had added earlier
On the first test run, the carb filter clogged after 5 minutes of running at 3000 RPM. I motored back at 1500 RPM and cleaned the filters.
I figured I was set into a mode of lots of filter changed and would try to burn off the gas as quickly as possible.
After thinking about it, I decided to speed up the process. I built a cleaning rig for about $200. The rig consists of a fuel water separator with bowl, an marine fuel pump, A 2 micron screen filter, switch, fuse, alligator clamps and about 25 feet of fuel hose and assorted connectors. I had to add a primer bulb to get fuel to the suction of the fuel pump.
I connected the suction of the rig at the outlet of my existing spin on water separator and set the discharge to the fuel tank fill.
I ran the pump for about 4 hours. I estimate that moved about 120 gal of fuel through the rig. It was a very interesting result.
First, the fuel was slightly cloudy and had a few flakes. It was also a dark amber color, sort of like dark olive oil.
After 4 hours, it was very clear and looked pretty much like light vegetable oil. a mild yellowish color.
I ran the boat after reconnecting everything, changing the on board spin on filter and carb filter (I flushed the fuel line that wasn't used as well)and went for a ride.
the boat ran much better. STBD ran to about 3800 RPM, which is a little off peak, and port was about 4200 which is fine. I ran at 3400 RPM for about 30 minutes before it started to bog. I moored up, checked the carb filter and I ha da little bit of gunk plus a little piece of Teflon tape that must have been on one of the fittings (I used thread sealant but PO had Teflon tape.
Ran the boat for another 30 minutes without any incident at 3500 RPM and hit 3850 or so peak.
Today I took the boat out again. Ran it for a solid hour at 3000-3400 RPM with no issues.
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The fuel was very cloudy but not discolored. I ran the rig for about an hour on a 5 gallon jug. After running it the fuel was much cleaner but not near as nice as the fuel on the boat.
Now the fuel on the boat was mixed 50/50 with valve Tec gas and ha da ton of StarTron in it.
I'm going to add some StarTron and try again. Basically, I think the StarTron really works wonders. From what I have read, it bonds the impurities allowing them to get filtered out.
So now I have a functional boat again. I will run this tank down low and refill with fresh again. I also plan on running the cleaning rig on the other tank just for good measure.
On a side note, I applied my rig to the fuel I had pulled from the boat before. On that fuel, the only additive was some Lucas Fuel treatment