I'm installing the ball joints but it appears the pass side had been replaced with a slightly larger ball joint by the previous owner. The BC one slides in with almost no effort. The driver's side fit just fine though.

I'm going to replace the knuckle, but while I wait for it to arrive(most likely the end of the week) can I run one extended ball joint and one normal length ball joint?

 

you can sure. But you're alignment will be out of wack most likely