Z-bar not aligned properly

The chances of every z-bar being perfectly in line from the factory is zero. The tightest tolerances on the chassis are the suspension points, even those were +/- an 1/8” and I doubt they were all in spec. Scratch that, I know they weren’t.

The ball studs actually allow for misalignment. If the clutch and pedal operate properly this isn’t an issue.

Also, that hole was sometimes drilled on automatic equipped cars. My ‘71 GT has a rubber plug there, it’s an auto with a console. If it was undrilled it would have a dimple in the inner fender to locate the hole. There’s a thread here somewhere with information on the hole for the ball stud. I forget exactly the conclusion but I believe it mostly determined the factory did all kinds of stuff and wasn’t nearly as particular as most purists suggest.