Those headers are desinged to fit with the engine in the stock location, I have them on many cars, and they fit well, maybe your trans swap has the back of the engine to low? Your doing a ton of work to re-engineer a superior design....
I did not change the mounts. The motor is in the factory location. We did change the rear crossmember to accommodate the Chevrolet transmission, but the motor is using factory mounts and OE frame mounts. They asked me what year block, what heads, what starter, etc ... and they hit the motor, the starter and the steering. And they hit the motor and starter while it was still out of the car. Not real happy with fitment. My old Hooker skid plates fit perfectly, they just hit every dime that was laying on the road and I couldn't access the back spark plugs.