You're going to have to be a bit clearer on your description. There are 3 studs with nuts holding your TB to your upper intake. There are also a couple nuts that have to be removed from the heads to get the crossover pipe heatshield out of the way in order to remove the TB bracket. Can you take pics of what bolts are giving you trouble?
If this has anything to do with switching to a Series 2 upper intake and TB like you mentioned in another post here, give up and put it back together. It'* not possible.