The following are the sensors that got replaced on both motors:
Engine Serial #0W000298

Crank POS #881667
MAP Sensor #881731
CAM POS #892615
IAC #862998
Intake Air Temp Sensor #805223T

Also replaced plugs and wires, starter and sea pumps

These were changed for preventative maintenance not because of a fault. The crank POS did end up presenting a problem in the wiring harness with the corroded pin, which did get fixed. The starboard motor was the initial transom that was found to be leaking and had the most corrosion on the back of the motor. I do feel that my problem is another harness or some sort of electrical connection that is not making good contact. But have searched and done the wiggle test and found nothing.

496 HO on-going issue - follow up
 

I started a thread on OSO regarding the engine breaking up last fall. BUP - had some good info to offer and thought I would see what your thoughts are for the following:
Now when I start the cold motor, I can turn the key and it fires but breaks up real bad. I can turn the key back off and immediately back on and it fires off and sounds normal now. Sometimes I do need to throttle it up and clear out the fuel and then it idles fine and runs fine. I did a fuel pressure check and it was right at 40. There is definitely a problem with it sending too much fuel (or not being able to burn off the fuel...spark) for it to burn off right away. I can tell it is the #7 cylinder and by looking at the exhaust flaps that side is not quite right. So I checked the cost of fuel pressure regulators and they are quite pricey to just replace. If I am correct, there is one at the cool fuel on the side of the motor as well as one at the fuel rail. Do you have any ideas?

Leaky injector on #7?

Try swapping that injector to a different hole, and if that doesn't do anything, try swapping the #7 coil to a different hole.

I replaced both with brand new.
Last time the boat was out it started rough. Turn the key off and right back on...started better. Rev'd it up a bit and it cleared up and was ok. Did a fuel pressure check and was 40-psi.

Turns out my ongoing engine trouble was from an exhaust elbow with a crack which was leaking water back into the manifold. Ended up replacing all four risers on both motors and one new manifold and the problem is now fixed! This has been an ongoing issue for quite some time and it's good to be back on the water worry free for now. Thanks for all of the suggestions and assistance!