I did a number of things, and the shaking, well, it's more of a bucking at the engine that it makes, right? I did get it down to, once in a blue moon where it bucks at the most random times during idle, but it's been once, maybe, a week. So in a sense, it's done
Before I definitely fixed it here's a list of things I replace and checked to see if it needed replacing before throwing in the towel:
1. Checked and replaced necessary coil packs
2. Replaced ECTS
3. Cleaning up IACV, TB, MAF and EGR system
4. Replaced spark plugs with NGK Platinums
Surprisingly though man, it was my sparks that were causing the bucking under load. And I went and swapped them out with NGK V-Power Coppers. I know, it's a step down from the OEM specified, but it helped. A LOT.
Do remember to make sure that no oil is inside of the spark plug chambers as it can cause detonation from time to time, which is probably why I'm getting that random single bucking, since I used the used set of gaskets that came with the valve cover when I did my 01VI swap.
To add to that, torque them down to specifications. On the box to it says to torque down to hand wrist strength and then 1/4 - 2/3 of a turn after, or just until the spark plug doesn't turn, but without using arm strength man. You can break it and then you're SOL.
I hope this helps man. And do hope you get it fixed