You might want to wait until you have the body fitted in its final location before fitting the side pipes. How the pipes fit in relation to the body (not the rails) is what matters and there is some adjusting of the body (pushing in/pulling out) to get the door fit right. I have a Gen 2 Coyote with the FFR catalytic converter headers and GasN Touring pipes and ended up using 1 small wedge on the passenger side and 1 large wedge on the driver side (from Breeze). Pipe alignment was perfect.

Your transmission cover looks great - where did you get the diamond stitch fabric?

James