Suggestions
I did a similar rebuild on a -4 with 700 hours of time on it. When I bought the re was significant cracking in the firewall and side skins around the lower firewall brackets. You?re doing the right thing - the lower engine mount attach brackets see a lot of stress for the landing gear, and the riveting of your old brackets would not have held up.
Here are some things I did:
I built a plywood box jig down the center of the aircraft to ensure things didn?t move. It attached to the floor structure and the roll bar mounting points, and allowed me to maintain location of the firewall, top longerons, and bulkheads.
If you don?t like the rivet lines in the #2 bulkheads, they?re pretty easy to replace while you?re ?in the neighborhood?.
Look closely at the firewall wedge to see if it was ?stretched? into place during assembly. The factory parts didn?t fit together very well, and stress during assembly will lead to cracks later. Replacing the firewall isn?t too much extra work with the sides opened up.
As originally built, my aircraft had binding and wear in the rudder pedal hinges. I found some really long AN bolts to span across each rudder pedal to eliminate the ?single shear? configuration of the short hinge bolts in the original design.
I added RV-6 style gussets to brace between the lower firewall brackets and the 3/4? angle uprights.
Good luck with the rebuild. It?s a lot of work, but well worth it!