D30 woes, gurus needed

I am in the process of replacing my balljoints. The passengers side joints were literally falling to pieces and the drivers side are being replaced just because. Now that I have the balljoints and knuckles in place, something weird is happening. The top of the pass knuckle doesn't come up as far as it used to. There is about 1/2 inch of upper balljoint shaft exposed, even with everyting tight. The drivers side looks normal.
I took measurements of the inner Cs and from the top face of the knuckle (where the upper joint enters) to the bottom face (where the lower joint exits), and the pass side is wider by about 3/10 of an inch. When both knuckles were off I had them side to side and the drivers side knuckle (at the joint mounting points) was narrower by about 1/4 an inch.
Everyting seems tight, but I haven't driven it yet. Could it be possible that I bent an inner C? Would it be ok to drive? It seems like structually none of the forces will be changed as the orbital motion of the lower balljoint can compensate for small angle changes. It's just that little bit of exposed balljoint shaft that is making me worried.

This is normal.

Just make sure everything is setted in place, the ball joints.

and all the nuts are correctly torqued. Also make sure to install all the cotter pins.

Put the jeep together and place it back on all fours, everything will seat into place.

hinkley