Maybe a hint here:
(A LONG time ago (when the CB750 was still King of the Road), it was popular to have the disc 'lightened' with holes like yours, and Cycle magazine (et al) was filled with machinist ads to have your disc drilled. Trouble was, if the holes were drilled and then heavily beveled (and not just the edges of the holes broken with a very light touch) the brakes LOST stopping power. It became common to have the holes just drilled (maybe in some pattern or another) and then the first set of brake pads were 'sacrificed' to quickly break in the disc. This worked well, but of course, Honda's pads were available everywhere then. Sometimes the 'fix' was to add the 2nd disc, but that's another topic...
(Fast forward again in my Wayback machine...)
Modern disc-hole-drillers are mighty proud of what their CNC can do for their egos, but I don't believe the physics have changed: I have noticed on a couple of cafe'd 750s that have resided temporarily in my garage that their widely-beveled-holed front disc (or discs) can't hold a candle to my almost-stock single disc (750K2), still OEM except for a straight(ish) shallow groove I added on each side to sipe away water while riding in WA State one soggy summer.
If truing the pads don't solve this one (because yours are barely contacting the disc pads' surfaces), maybe consider getting a new, sharp countersink and touching the holes to raise a slight edge on them at their tops? This edge will quickly wear off, but will also true the pads to the disc face(s) where it counts.