engine/trans vibration

I had to shim my engine up for TTI clearance on the 1970 K-frame; 1/4" per side minimum. I made some flat-iron plates and torched a slot into them, and slid them in there,not pretty but functional.
I had all sorts of issues when I installed 2 years ago, Had to shim one side, had to ding in the pipes to fit (made me cry to dent such nice units) in several places: PS steering shaft coupling, drivers side frame, passenger side torsion bar, I had the header in and out numerous times....... may be I shifted the engine slightly when removing/installing the rebuilt trans.....I know I have several very close areas where the header pipes may hit....