Clearance windage tray around main caps?
 

'67 400, 4" Scat crank, Pro-Gramm main caps with ARP studs.

3/4 length Tomahawk windage tray, Canton oil pan.

Issue is the windage tray hits the ARP studs before the retaining bolt holes mate up with the tapped caps. About 3/8" standing off, too much to shim IMO and besides, the tray hits the oil pump at that height too.

Do I drill out the tray and let the ARP studs poke through?

Yes, you can drill it out, but do it in steps up to the needed clearance for the 1/2" studs.
whike your at it round out any sharp corners in regards to the sheet metal as these provide places for cracks to start off.