It may be just me, but I would clamp both 2 X 4s together so one end has them even and then cut them BOTH to 60" as the instructions say, then drill the holes through BOTH at the same time to insure that they are the same. That way, it's easier to insure that they're both in alignment. Also, make sure you make the diagonal measurements equal before you tighten everything up for welding when you put the pan back together.
Just as an aside, I have found it a LOT easier to carefully cut the welds holding the cable tubes to the chassis at the rear of the pan so they are then free, then cut the section out of your pan and just push the two sections back together, now shorter. THAT way, you're not messing around trying to get the tubes back together inside of the tunnel. There should be 6 tubes to deal with: (2) heater, (2) emergency brake, (1) throttle and (1) clutch