Thanks very much for the post. I am about to go through this same thing. I agree about the cheating. But, you are literally cutting a structural component that is integral to the vehicle chassis. There must be a better way than that!May be time consuming, but there is no reason to try to cheat.
that has to be modified manifold, I had to cut off quite a bit from the bottom of the collector and even then I had minimal clearance
No. The manifold has to be from the engine being swapped and cannot be cut or modified in any way. Smog ref who is very familiar with these swaps has been helping me overcome every CARB requirement. It was very tedious but possible. There there was a solution for every legal requirement.
Notching cross member is major one people usually try to skip.