To summarize: if you are waitlisted for CPU and the CPU doesn't clear within the window while R>0, the only (productive) thing to call UA about is to make sure *your* reservation is not out of sync. If your reservation is fine, then you are stuck waiting for the computer to do its thing. UA agents will not clear your CPU.

When using an instrument however and R>0, you can do the "remove the instrument and reapply" maneuver, and that is worth a call and that should get the upgrade confirmed for you, potentially skipping the waitlist queue.

I think the strong reaction to the OP is that this scenario (waitlisted for CPU that doesn't clear within the window while R>0) has been so common over the past 3 years that it's old news. Few are happy about it, but we've adjusted to the ways of this new system. Perhaps the OP has been lucky and it hasn't happened on routes he flies, and he's now going through the freak-out that many of us did 2-3 years ago, in compared to the PMUA system we had become used to. And in this case the OP was lucky and got the upgrade at T-96. Many times in that scenario it won't clear till T-24, at the gate or not at all. Just one of the MANY things that changed from the days of the Tulip.

Also, as relates to the DL/AA comparison, I think it's worth pointing out that not only does DL not have transparency of its upgrade bucket, they don't even allow their revenue fare classes to be displayed on sites like EF.... Which in some ways is more arrogant and customer-unfriendly than these UA upgrade glitches, which have lingered now for 3 years and while certainly imperfect at least offers some benefits to those with the time and patience to closely monitor their flights.