Dennis,
The challange is that with the suspension assembled to the knuckle the bushings are under tension, so they do not really align correctly. BE VERY CAREFUL, do not force the bolts in or they will crossthread. Sounds like you are being cautious. Would I be correct in stating the two bolts are for one of the bushings, and the other bushing bolts are in place?
I am relunctant to make this suggestion, but you may need to separate the upper ball joint, then reinstall the upper arm separately, then reassemble the entire suspension.
I am thinking you took these out to get more clearance for the shock R&R, and as soon as you got the bolts out the upper arm bushing cocked slightly.
If you have tried raising the suspension knuckle all the way and it will not align, you may have to do what I mention above. Please seek additional comment on this, maybe someone here has a trick.
If you do need to separate the ball joint you will need a special tool to do it.
Good Luck,
HTH,
LarryB