Here is the background on the current set up
engines are original 454 Mercruiser twin turbo 475's. Running a drawthru from a Holley 750 to two Rayjay turbos.
Both engines are set up like this
Primary 80 jets, 5.5 PV that is boost refrenced
secondary 100 jets 5.5 PV that is not boost referenced
No choke, float levels in all bowls have been checked.
OLD mercruiser CDI ignition box connected to a T-Bolt distributor and a Nutek Sizzler coil. The ign box is mounted to the firewall, It is not the T-bolt style of control module or even the standard T-bolt style amplifier.
This is how I got the boat and it seemed to work before.
The port engine is the one that runs good and doesnt have issues. Per the manual the total timing is 28 deg and 16 inital, BUT that was when it had a points ignition. It now has the T-bolt dist body and a ign control box. I opened the sides of the ign box and see it is completely potted and does not have any adjustment pots of dip switches.
The port engine starts great and will idle well I can get the port to go into gear. In gear it will idle at 745 rpm at 14 deg of timing and 11 in HG vaccum. In neutral out of gear it will idle at 1100 rom 25 deg of timing and 14 in Hg vaccum. Why the timing moves around is beyond me for a box with no adjustments (unless its preprogramed and not adjustable)

The starboard engine is a different animal. Same exact carb jetting and PV. Timing is set at 25 deg at 1100 in neutral. If I try to put the engine in drive it instantly stalls, If I try to do this on land, it will go into gear so I know its not a locked up drive. Ive gone thru this carb and cleaned it all out. I did switch the good carb from the port engine to the starboard engine and the engine started right up on land, did not try it in the water though. AT this point Im thinking its a carb issue, but things looked ok in the carb when I went thru it. The timing also baffles me.
​​​SB , I have not switched boxes to try it out but will have to also try than.
The below picture is the ignition control box. There is no other module used

UPDATeE: I found out that the secondary throttle blades on the one engine that would not t\run correctly were open too far. I swappped carbs and water tested the starboard engine with the port carb and the satarboard engine ran great. So i took off both carbs and compared jets, power vlaves squiters and everthing. The parts we all the same. It wasnt untill I held the carb up to light and looked at hom much light was coming thru the secondary throttle blades that I noticed the problem. On the good carb the edge of the secondary were 4 mm from the edge of the baseplate and on the bad carb it was 5 mm. I looked at the secondary blades screw and it was turned in farther that the other carb. I ended up turning the screw around so I could adjust it from the top. Put the carb back on and and adjusted the screw to it was 1/4 turn from keep the secondary blades completely closed. I ended up with the secondary blades just a hair from completely closed so the engine did not die when I put it in gear. Now both engines idle at 950- 1150 in neutral and in gear about 750 rpm

Thanks for the update and glad you found it. I would have never thought of that. I had a similar thing happen to me on my old Scarab...turned out to be a bad coil....not sure why a load on the motor made it stall but it was doing the same exact thing...idled perfect and rev'd great in neutral but as soon as its in gear with a load it stalled...i was swapping everything from left to right untill i got to the coil and the problem followed. My guess is the spark wasnt strong enough in gear to light it off properly??? i dunno