there is something seriously wrong with that set up. weather the motor is in the wrong spot or the headers are not for his application. my tti headers went in without having to even slightly ding them.
You aren't dealing with torsion bars though. Granted most people it seems don't have much of an issue with the install outside the standard head aches.
I have to agree with the others that are wondering if the OP has the correct motor mounts.
To short of a mount would close the header/steering clearance and probably put the pipes in the wrong spot to clear the torsion bars.
For your sake i hope its a QC issue on their end and not something else.