GT40 EFI engine vibration

I got that issue sorted and just this week also fixed the loping idle issue that has persisted since distributor and TPS replacement by swapping out the ECU. 

Prior to resolving the idle loping, I have had issues with the boat occasionally stalling or almost stalling at times while shifting from neutral to in-gear. Sometime there is a bit of clatter if rpms are too low. I just endured this for last 3-4 weeks. 

Starting about 3 days ago, the engine has developed a concerning vibration. It exists in idle and under way so I assume it is engine and not drive train related. You can feel it in the floor, steering wheel and throttle lever. If you have a bottle of water in the drivers cup holder, you can see the ripple in the surface. It does increase slightly with rpm but not significantly. Its not horrible, but since I can detect it so easily, its also not minor. 

I've scoured CCF and come up with various causes from exhaust issues, to misfires, to valve seats to damper plates. 

Tomorrow morning I'm going to go buy a compression gauge and do a compression test. I will also use my timing light to test spark signal. 

One question I have that I am not clear on. Can a bad damper plate cause vibration at idle? 

Also, for reference, the transmission was replaced 48 hours ago at same time as engine rebuild. It was replaced with one of the last 40i trannies out there (I know I should have gone with 80, but rebuild at same time was a lot and I got a killer deal on the 40i at $650). We should have prolly replaced damper plate at that time but I was not educated on them at the time and no one helping me mentioned it. 

So, is a damper a possible suspect? And what else should I start checking?