2005 322 - Erratic RPMs with 350 Merc

[JimE 0]

I have a 2005 Monterey 322 with twin Mercruiser 350s.  The engines are both about 3 years old as they are replacements of the original engines. 

Ever since I got the new engines the starboard engine has always had erratic RPMs.  It isn't so erratic that passengers can feel it but if you are driving with your hand on the wheel and you are watching the starboard tach then you can "feel" the subtle variations in power matching the small movements of the gauge.  The port tach stays dead-on whatever I set the speed at.  It doesn't move a pixel.  If I get up to speed and the engines are both running at about, say, 3,600 RPMs the starboard RPMs can "wander" as high as 3,700 or as low as 3,500.  Again, they aren't sharp changes you would feel as a passenger.  It takes seconds to occur.

I use 2 mechanics...one for really big jobs, like installing these new engines, and another mechanic who does everything else from small to bigger jobs.  Unfortunately, the mechanic who installed the engines passed away so my "daily" mechanic is trying to figure it out.  He is a very good mechanic but hasn't figured out this conundrum yet.  He has adjusted the timing (it was a little off), checked my cap and rotor, replaced the IAC valve,  cleaned the throttle-body and done all of the regular maintenance.  The issue still occurs.  The mechanic says the (pardon me while I butcher this) that the caps/rotors on that engine get dirty faster but not enough to affect performance.

The engine has generally run just fine for 3 years except for this slight issue.  It always runs but this slightly erratic behavior is a little unnerving .  It was a "crate engine" which means parts from the old engine that were still good were put on this new engine (alternators, starters and the like).  The port engine, also a crate engine, runs perfectly.

My mechanic thinks that it is possibly that the engine may not be firing correctly.  I saw another post on this forum from someone with a similar issue.  They were told to check an oxygen sensor but my mechanic says my engines aren't new enough to have that sensor.  That other post said some valves may not be "sealing correctly" but my mechanic thinks that issue would cause a much more severe problem with the engine than mild fluctuations in RPMs.

I'm not mechanically inclined but pretty smart at figuring things out as I'm in IT.  I'm suspicious of the throttle cable or an electrical issue.  The other mechanic did put in a new wire harness and the boat is 15 years old run in salt water.  Could an electrical or wire harness problem or bad connection do this?  

Would love to hear everyone's thought!

Thanks!

Jim