A lot of work 3 years ago for me, many of the same problems. My collectors are way longer than yours, the flange clears the crossmember by 2".

The collector tabs on the passenger side hit the trans case, and are nearly impossible to bolt up. I thought this was a manufacturing error on my set, but obviously it is a shameful engineering error. They apparently did this to avoid having to build opposite hand collectors.

You didn't mention having to re-route the fuel line and starter wiring.