I read billavista's article about driveline angles. I didnt see anything that talks about what happens if I have a CV but the pinion yoke is pointed higher up than the output of the t-case. I lowered the truck 4 inches after having set the pinion angle already. The difference is greater than 3 degrees.
Is the driveline going to shake or am I going to snap u-joints ?

You'll eat u-joints. Just put a shim in and fix it.

Yeah you will eat u-joints, like said above shim it or reset the pinion angle again would be the best thing.

Thanks, my shackle ended up being too short. I put in the longer shackles and it got back the degrees that I needed.