Couldn't get this right today. Everything is lined up good but when the hood is closed the rear is a bit too high. Which bolts need adjusting to get that down?

Cut & Paste from the resto Rick site... Works on more than E bodies..

common alignment problem on E-body & 71-up B-bodies is with the rear hood edge being up too high with the hinges being adjusted all the way down on the inner fender.
This is an adjustment problem! Start by moving the hinge up on the inner fender. (yes, up!)
Then, loosen the 2 rear bolts and leave the front bolt snug. Now lift the hood to make the hinge rotate (as viewed from the side). Retighten the rear bolts and check the fit. This procedure will get that tail to come down. Adjust the front-to-rear dimension on the hood side bolts.
It can be frustrating and take some time, but these hoods will fit correctly! I’ve installed them with the hood sitting about 2 1/2" above the fender...using this method, the hood was fitting perfect in a few minutes!

I'll give it a shot.

Following the advise above normally cures that problem.
On two occasions, we've seen the arms of rebuilt B-body hinges bind up when closed. This will also make the back sit high. The only solution was to order replacements from the rebuilder.