A couple things......First, have you made your 12 year gate yet? If you have and you are good, IIRC you have to have 8 years of flying to be good at your 12 year gate, you should be eligible to get flight pay out to 18 years. When I made my 12 year gate in the reserves I got a letter from a GS at NAVRES saying I was good (not sure if active guys get a letter?). I gave it to my RESPAY officer and all was good. If you have not made your 12 year gate yet you should be good if you are still designated an Aviator/NFO up to 12 years. If you are past 12 and didn't make our gate I think you are SOL. If you are past 12 years, think you are good but don't have a letter saying so I have a 2 year old POC for the NAVRES guy if you need it, he was a bit short but gave me what I needed. All this was based solely on my experience, which seemed to be the norm.
As for taking a drill to do your physical, by all means do so. I took 2 drills for my first two physicals in the reserves because they took so long, mainly because it was so backed up. This last one my new CO, a former VP squadron CO, said the rule of thumb was to take only one so that is what I did. Not sure what the other reservists here did, but you definitely rate at least one paid drill for the physical.
As for administrative snafu's, they seem to happen a lot more in the reserves than they ever did on active duty. You really are the only one looking our for your career and you have to make sure everything gets done on yourown, from pay to Fitreps and everything in between. There are quite a few reservists here, current and former, so it is a good resource if you have questions.