1) I have found several GAs that believe existing upgrade lists should be cleared before adding standby passengers that could trump them due to status. This is not the rule and not the way the system works. The trick is finding someone else that can/will put you on the upgrade list and let the system do it's job. Some have reported kickback with the original GA negating the change and removing you from the upgraded cabin. My guess in your situation is GAs may not see many PAID tickets on this flight and that didn't register like it should have.

2) You should get the EQPs for the fare paid. I'd start with a phone call to try and get this sorted out. If that fails try a short/sweet email to CS to research.

3) Yes, it does take a few days for the numbers to process. The fact that the counter has dropped tells me it's in process. Hold out a week or two and then call, unless you need them sooner. The back-end systems do get updated quicker than the front-end so you may be good to go already.