2002 Formula 27PC with twin 4.3L MPI's. We were cruising for an hour or so at around 3200 RPMS, I throttle up a little bit to go even faster, and suddenly the port motor starts loosing power and develops a slight knocking, so I backed off both throttles, and they both idled fine with no knocking anymore. Try to get up on plane and both motors begin knocking and we are not able to even make it on plane. Come back to an idle and knocking is still there on both motors at idle. Shut both engines off and check for any signs of damage and check all fluid levels. Port motor was around a 1/4 quart of oil down from when we left, but everything else was good. We started the starboard motor back up, and the knocking was still there, but less audible. We begin to idle back to port on just the starboard motor while I try and do a further diagnosis on the port motor. after about 5 minutes the knocking on the port motor goes away. So we started the starboard motor back up and it is no longer knocking either. Now both engines are running with no knocking so we got up to about 2500 rpms and cruised there for a while back to port. Once we were close to home we throttled both engines up to around 4000 rpms with no issues.

Thinking the engines were starving for fuel and caused the knocking. Does this make sense? The only thing that both engines have in common is the fuel tank, and both motors had the exact same knocking sound, and they both started doing it within 30 seconds of each other.

My only other that is because we were running pretty hard for an extended period of time the oil became to thin and no longer was pumping up the lifters. I dont really think this is the case though because oil pressure was good the whole time.

The knock was definitely coming from the lower part of the motor. Almost seemed like it was coming from the raw water pumps, but not sure what inside there would making the knock noise I heard. At one point it almost sounded like an engine "dieseling"

Any chance of having a video of it to share?

I wonder if you got a bad load of fuel ? Maybe water in the tank ? Did it happen when the tank was getting pretty low ? Both engines off the same tank I assume ?

No, unfortunately not.
It wasnt as loud as a rock knock, but louder than a tick. For sure was louder towards the bottom of the motor than the top.

Tank was around half full (60 gallons) but I am unsure of the condition of the fuel. Both engines do run off the same tank, but the tank has individual pickups on it.

With no alarms or signs of problems from a visual inspection, you probably are looking at a fuel problem especially with a loss of power.

Check your fuel filter(s) for signs of water.

I drained the fuel filters into a mason jar yesterday and the fuel looked clean with no signs of water. Today I ran the engines each for about 30 seconds to verify idle timing, I then pulled the fuel filters again and poured the gas into a mason jar. This time the gas was brownish color and full of sediment, no signs of water though.

Kind of odd that the gas was clean the first time I pulled the filters, and not the second. The first time the gas in there was from the engines running on the lake, the second time was after the boat sat in the shop for 4 days. Im pretty sure there was about 20 gallons that sat in the tank unused for around 2 years. At the beginning of this year an additional 40 gallons was put in. Another issue we had on the lake was the port motor would not get past 3800 rpms, the starboard had no problem spinning to around 4300.

Sounds like you found your problem. Time to drain the tanks. I would also probably get your fuel injectors out for a good cleaning.

Yup, except the owner of the boat filled it up before I took it out of the water. There is probably 100 gallons of gas in it right now..

Detonation can be knock noise. Same with preignition. Not always just a rattle.

Sediment in fuel is no bueno.