re3.5 lift install question

My dad and I installed a 3.5 inch rubicon express lift (with full packs) yesterday into his 93 4dr xj, went pretty well , only one hole cut into the beast for the front leaf nut that spun inside the frame. We got it back ontop the ground and something was making a horrible thump just moving it around in the shop. We put it back upon the hoist and found the front driveshaft yokes ears were making contact and binding the driveshaft. Anyone come across this?? We just clearanced the slip yoke and it seems fine. Wer notice a slight vibe at 10-15km/h but thats it, no vibes at highway or accel or decel. I don't remember this with my 89 at 4.5 inches of lift when I had my stock shaft?

Did you do a TC drop?

no drop, no shims, no vibes after clearancing.