Yes you can drill them out to match them. No confusion there, but if you radius the entry hole it will act much leaner or bigger if everything is not identical. The depth of the hole will effect the bleed as well. some bleeds have to be drilled all the way through about 1/4" total depth, and some only require about .030 depth to get to the other side of the bleed. No biggie either way that creates a minor change. You may look at to see of you are running less fuel pressure than on the dyno too. The lower fuel level can make a lean hole when the booster tips in off the idle / transition circuit. Go about 4 hundredths smaller on the bleed to test, that is about the same as a jet change on holleys and enough to tell if you have the bleed too large quickly. I have never done part throttle pulls on the dyno before but you may have had this condition you are fighting present on the dyno, but did not show itself and behaved like you said it behaves when you slap the throttle and runs fine. The power valve may be too low a number and causing a lean condition in the car that the dyno would have never measured or known because it was wide open flowing fuel the whole time the test was run, not part time like on the street........... Good luck hunting, if you have reason to believe that the bleed is drilled bigger than what you dyno'ed with than you are likely correct on the fix but driveability problems are common on dynoed engines that do not run at wot like they are tested.
Bruce