I have control arms on the way from Clayton Offroad to fix the problem but was wondering with the front pinion being off 5 degress how bad of vibrations will this cause? I just installed a 4spd atlas and it moved the yoke on the t-case about 1/2" closer to the front end and moved it up a bit higher due to the way we clocked it, and after installing my new driveline I took it out and drove it and when I hit about 30mph it started shaking horribly, the rear angle is dead on. Oh and its a 2002 TJ if that makes a difference.

I have control arms on the way from Clayton Offroad to fix the problem but was wondering with the front pinion being off 5 degress how bad of vibrations will this cause?

30mph it started shaking horribly

I think you answered your own question. Pull the front shaft until the arms are installed.

with no front shaft, it vibes at 30ish, and the rear pinion angle is "dead on"?
whats your question, again?

without the front shaft there are no vibes. I was just wondering if the pinion being off that amount could cause bad vibes or it maybe my new driveshaft has a problem (Its a Tom Wood's). Yes I pulled the front shaft immediatley, and my new control arms should be here on thursday.

did the splines disengage when you put it on/pulled it off? could it be off a spline? that would make it out of balance.
or maybe the u joint caps are hitting the yoke if it is at an extreme angle...?