Mechanical gauge right in the plenum as well as reading it off the MAP sensor

Bravo boat? Bad coupler maybe?
I know you said the lazy engine won't rev. But on the flip side, no load no boost for the most part.
Other than that, fuel issue? Are all the fuel components you dyno'd it with the same as in the boat?

Yes Bravo boat with brand new couplers. Engine will spin up to 4000 rpm and at that rpm should be making around 4 psi boost. If the procharger is spinning at that rpm it HAS to be making boost - its a mechanical pump that's driven by a belt off the crank. Anyone know if there's a way to actually test the procharger? We've done a leak down on the motor and everything checks out perfect. Either the blower isn't producing boost or its being lost somewhere. I've pressure tested all the tubing and the chiller and there's no leak.

You already switched blowers from side to side if I'm reading right, correct?

And no it doesn't HAS to make boost. Put a open ended tube from the supercharger just into open air with a pressure gauge in the tube, spin the thing 50,000 rpm and Ill bet you see no "boost" on the gauge.
So the boost seen in the past on your gauge on that engine was the gauge pressure seen at a typical rpm with a typical load at that rpm on the engine.
Got a turbo'd diesel truck with a boost gauge? Drive along flat ground at whatever speed, make note of the boost, hit a steep hill and don't downshift or let it downshift, try to maintain that same speed, watch the boost rise.

Otherwise, have you tried at least to run both N/A with out the belts, see if you can achieve the same rpm on each engine with the same props?
And yeah I'm aware the tune may be off running N/A

"Bad" side isnt making boost at 4800... What RPM is the "good" side making boost?

Yes blowers, chillers and all connected tubing was swapped from sure to side

i have not tried running them N/A but I will try that. The problem is actually on both motors - not just one as originally thought. We have hooked them both up to a computer and one will spin @ 4000 rpm and reads zero boost off the MAP sensor and the other motor will spin to 4300 rpm and reads 1.7 lbs boost off the MAP sensor.

The problem is actually on both motors - not just one as originally thought. We have hooked them both up to a computer and one will spin @ 4000 rpm and reads zero boost off the MAP sensor and the other motor will spin to 4300 rpm and reads 1.7 lbs boost off the MAP sensor. Prior to this issue they would run 5200 @ 5.5 lbs boost

The fuel you are using is crap and the knock senors pulling them back? Just throwing out stuff because I don't think there is much left