"yep. you have discovered another early car anomaly.....keep digging there are more."
It's not an "Early Car Anomaly".... My Late production '65 and my '66 both have the same identical "Cut-Outs"....
The "Cut-Outs" are for the Brakes hoses.....so that the Brake Hoses don't get crushed by the Tire against the Uni-Body Frame...
I believe that "Really Early" cars don't have the cut-outs.... Like Dearborn Mustang#1 VIN# 100001 ..... No Cut-outs on that car...
Others will chime in to comment...
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Tony K.