The problem is fixed. After lots of head scratching and help from you all at classicparker, here is how I got it figured out:
Like I said in the previous posts, I continued to monitor the engines RPM and spark plugs in hopes that the problem would eventually reveal itself and it finally did.
The initial steps that I took were, compression and leakdown tests. These tests all passed, I don't remember the numbers.
I also replaced the spark plugs. I put a couple of hours on the new plugs (Max rpm 5500). I got home and checked the new plugs. the stbd bank had dirty plugs, while the port bank was super clean and barely looked used. I also looked into the cylinders and noticed that the port bank looked brand new, and the stbd bank looked dirty, just like the plugs. This made me think that my injectors were either bad or dirty, because the port bank was getting flooded with fuel.
Couple of days later I decided to run it again, this time 5100 max rpm. I got home did my normal routine, check plugs, cylinders and oil. the plugs and cylinders looked the same, but the oil had risen. So it had started to make oil as well. The fact that it was making oil, confirmed to me that the cylinders were getting flooded. (port bank) The gas from the flooded cylinders was running passed the rings and into the oil pan, thinning the oil. (stbd bank) The gas thinned oil was able to travel pass the rings on the combustion side and foul the plugs on the stbd bank.
So, I pulled my injectors, VST filter, and engine mounted fuel filter. I took my injectors and VST to local shop and had them cleaned. While they were being cleaned I decided to go ahead and change out thermostats. Low and behold the port thermostat was stuck open. I know that a stuck open thermostat will cause an engine to run cold and flood the cylinders, so this could have been my initial culprit. I got the injectors, and VST back from the shop and the shop said they were all super dirty especially, but they were all able to be cleaned.
So I reinstalled the cleaned injectors, VST, new thermostats, new fuel filter on engine, new 10 micron filter, removed all of the old gas, and changed the oil as well. I was finally able to take it out this past weekend and run it. She ran like a champ, 5800 rpm and the plugs looked great.
