You can match that little bit and grind it if you want, if you line it up before tightening the bolts it won't be like that.
As for the w/p's, this is how to tell a higher flow vs a standard flow pump tight is high flow, a gap like the flowkooler is lower flow...
FYI, flowkooler now has one...
My advice would be to replace all bushings and start over with the balancing to confirm things are in spec.
If 1 bushing was damaged you may not notice the others are until it's too late, build once and have piece of mind...
Yes the pics are gone but all the parts are still on eBay...
https://www.thetruckstop.us/forum/threads/diy-charge-air-cooler-under-400-00-for-all-gmt400-trucks-subs.38704/post-441543
Wear on the entire valve train... weak lifters, ware on rockers, ware on valve tips, ware on valve seats, week springs....
It all loosens the preload on the lifter, say new preload is .050" new .. now you may have .020", the wore out lifter doesn't stay pumped up as well...
The fact you stated...