Vibration on acceleration

I just bought my 89 wagon 2wd and decided to swap the drive train from my hatchback into it to make it a little more fun.

Drive train consisted of
Turbo b16a
Ebay motor mounts
Ls cable trans
Ls hubs
Passenger b16a axle
Ls integra half shaft
88-89 integra drivers axle

Before I did the swap I had no vibrations at all from my lowered hatchback. Now that I put it all in the wagon and lifted the wagon 2 inches I finally drove it and it vibrates like crazy from the driver side on acceleration.
My ball joints and wheel bearings are fine and my axle shafts aren't torn or have much play in them.

I did notice my drivers axle was slightly too long and bottoming out in the half shaft. I swapped out my half shaft for the shorter ls half shaft.

I also noticed my driver side axle seems to be on a decent angle towards the back of the car

I am just beginning to go crazy and was hoping for some insight or help on the situation. I couldnt find very many threads about a b series wagon that's lifted having similar issues. I am just trying to get rid of them. Thanks for any help
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