You're causing yourself triple the work by having done the intake first instead of just keeping the intake put away until you got the heads and/or cam to go in with it. You're going to have to rip it all apart AGAIN. The cork or rubber front/rear lower gaskets are fine as long as you're using a stock intake. Otherwise, lay down a fat bead of RTV. Leave the TPS right where you left it. It's not supposed to be messed with unless it is out of range by a large margin. The screw you referred to as an idle screw is just a throttle stop and was not meant by Ford to adjust the idle. Be sure that it was backed all the way out before you set your TPS to the mid .90 range. I hope you're replacing factory bolts with ARP pieces as you go.