So I'm in the middle of threading the bolts thru the TB and plate to the manifold, when I realized the top bolt isn't going through. Pull it apart to see if its not aligned and sure enough, the plate doesn't have a hole for the topmost bolt on a 90mm setup. Is it supposed to? And if not, I take it using just 4 bolts seals it well enough so I won't have a vacuum leak? Thanks.

 

Four bolts is all you need.

 

If you look at the plate there is an indention where you can drill for the extra bolt. It is not reallt needed though. These plates are designed to work with the 90mm and LS2 applications.
Dave