Seriously, I can't imagine that there would be any substantive difference between the ZF and Audi gearboxes with respect to intrusion from the headers? The supports for the mufflers might have to change of course, but that's simple fabrication work. The actual architecture of the headers is primarily dictated by the engine, suspension (swaybar configuration) and bodywork.
At one point I purchased a set of CAV headers to fit to my KVA as part of what was to be a switch from a Porsche transaxle to a ZF. What I found was a) the crossmember between suspension was in the way b) engine in my KVA was obviously positioned higher than in a CAV so the rear clip would not close. It was going to be a major surgery to drop the engine and ZF, so that idea died, but in principal the CAV headers fitted the 302/ZF combination, just check geometry for any crossmember support or sway bar.
When I built my one-eighties, I found the 930 clutch slave cylinder to be an issue that didn't exist with the Audi box. In your case, I'm guessing the bellhousing area is less intrusive on the ZF, than the more sloping Audi box (again, dependent on where and how tight the headers follow the pieces). Is it inverted? This changes things a lot as well.
One would think that the headers would be the same for both. I guess I will just have to see. I'm assuming the angle over the cross support would be the biggest issue because either setup will still be made to come out the back of the body work at the same spot. Does anyone know if a zf gearbox is taller at the bell housing then an audi ? If the Audi is taller then no issues no ?
The level of the output flanges is below the input shaft on the Audi 01E and above on the ZF, this means with the ZF the engine can sit lower in the car and I *think* the ZF will be taller than the Audi