Help! Intake manifold won't fit!

I did that exact job on my 66 Barracuda last weekend and had the same issue.
The bolts secure to the heads and they're angled. The thickness of a new gasket is the issue...you have to align it perfect and catch a few screws on both sides, but don't draw them in till you have them all caught.

When the gasket is compressed, they line up perfect.

I didn't want to disturb the timing and left the distributor in...the last bolt was a pain to get at with the throttle cable bracket in place. You could draw down all the bolts, then pull the last two to add the bracket. Ultimately, you'll need a 1/4" drive ratchet with a 9/16" socket to get that one.....if you chose to do it my "back assward way"