You should loosen the bolts on the crossover, the 2 going to the front log and 2 goin to the rear log, then loosen the bolts on the turbo. Once everything is loose, things should be pretty easy to adjust. Move things to bring up the downpipe a bit or where it needs to be. Then start tightening one at a time, making sure it still has room.
I would use some header wrap and wrap the harness of the trans that is directly below the downpipe that may be touching. It would cause some trans problems if the harness gets melted.
The IAT sensor usually only adds or takes away a couple degrees of timing. If it were plugged in and is in your engine bay, it probably will sit at a high temp. It would only take away 2* max in very hot temperatures. I wouldn't worry about it as much right now because it usually doesn't work to put it in the intake and not have it leak past 5psi. They might have zeroed out the IAT table in the pcm anyway. Here is what it looks like stock:
