Ouch!

That's why it's important to fit everything up before final welding.

If by cab brace, you mean the inner-to-outer cowl piece, that should be pretty much flush with the outer cowl panel, although there's room to move it if needed. Your third picture seems to show it sticking way too forward to be able to get the fender mounting holes in the outer cowl thru it without hitting the back section of the inner-to-outer cowl.

The rocker panel mounting is located using a really hard to find dimension in the FAM, but the parking brake reinforcement should fit fairly closely with the toe board and the rocker. See the attached pic.

As far as the holes on the passenger side rocker and inner-to-outer cowl piece, I think they just put the holes in the blanks for the parts and then stamp a left and a right. Those holes don't really do anything, except help line up the two parts.
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Kevin
1951 Chevy 3100 work truck
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1929 Ford pickup restored from the ground up. | 1929 Ford Special Coupe (First car)
Busting rust since the mid-60's
If you're smart enough to take it apart, you darn well better be smart enough to put it back together.