Before you go blaming the balance on teh shaft, have you checked your installed angles on your ujoints with the new shortened shaft ? it shouldn't have made that much difference, but you need to check, just to be sure. If your angles are too much, or too little, it will shake itself to death. the position of the output shaft of the new tranny will change teh geometry of your setup a bunch. If you PM me your email address I can send you the spicer Ujoint allignment guide
I appriciate the offer, but I am 100% it's a balance issue. I am goign to PM you anyways jsut in case.
I blocked both front tires, jacked the rear up, and set it down on jack stands. Then I put the tractor up against the front of it in case it decided to get up and run away.
I fired it up, put it in 4th and went under to have a look....it was WAY out of balance

. It had like a 3/4 = 1" wow right after the steady bearing...which I feel is a LOT!!!
I will know for sure if that was the problem or not as soon as I drop teh shaft off tomorrow. I might end up lowering the tailshaft 1" by offsetting the crossmember and gusseting, but I don't think it is an angle issue....they are almost identical to my buddy's 351 gasser 5 speed 2wd truck.