H/Divine, I'm practicing, trust me
Lemme tell you a story...
Last year I took up the (soprano) clarinet again. Last time I played before that was 30+ years ago. Anyway, I had a similar problem where certain notes just wouldn't play without squeaking. After two weeks of practice I couldn't get better results. So my teacher looked at the horn very closely and discovered a badly seated pad --- a leak! Once that was fixed I had no problem playing in all registers. So the moral of the story is that it's not always a matter of practice. Sometimes it's the instrument. And Hump confirmed that the problems I'm having with my bass clarinet is typical for that instrument. So the next step for me (aside from continuing to practice) is to have a woodwind tech look at it and possibly do some modifications.
Hump, I contacted a well-respected bass clarinetist/woodwind tech on the east coast who's going to do some modifications to the keywork for me (which have nothing to do with addressing the upper clarion problem). I mentioned to him the things you suggested regarding the clarion problem (undercutting tone holes and so on). His first thoughts were that the register tube might need to be looked at, though he said that uncutting the tone holes could indeed help response in all registers. He said that that job would be difficult, though, because ABS plastic doesn't file well; it tends to crumble and form rough holes as opposed to the smooth results that could be achieved if doing the same to hard rubber or grenadilla. But I'm going to have him look at it all the same and see what he has to say.
And he also suggested that I try stiffer reeds.
In any event, I continue to practice with what you suggested in mind. It's been a great learning experience so far.
Cheers!