I am replacing the Hookers with the correct exhaust manifolds and to my suprise there are two holes real deep on the passanger side. Could someone explain what type of bolt goes in those two holes. Thank you.

2 deep holes in the manifold itself ??? theres one not as deep on the drivers side also , TUBE nuts go on them .

you need studs in all the holes in the heads , especially on those 3 holes , or really long bolts and fender washers but i doubt you'll get a good seal on the gasket surface .

also set the manifolds on a known flat surface and see how badly they are warped , getthem planed at a machine shop or you;ll be chasing an exhaust leak like another member did ...

You can find the correct ones at Mancini Racing:

http://chucker54.stores.yahoo.net/oemexmastnu.html

Hardens will sell you just the 3 long nuts.I just replaced my drivers side,due to it being cracked in half.If you want some KILLER gaskets.Go to remflex .com.My buddy told me about them.They are exspensive,but they are by far the best.They are 100 % graphite.They are 1/8 " thich and you compress them 50%.They are NICE!!!!