Unless it's changed in 3 years, for the medical I went to my doctor and after he was done laughing he filled out the medical form. For the background check I used the FBI website. I needed to get fingerprinted at a post office offering the service. Usually I'd get the results via email within a couple of hours.
Same here last year but this year I chickened out and paid for the stamped version. Next year I'll have both versions and try the app version first to see if it's accepted again.
I did not get a new 90 day report with my extension (CW). In fact they were explicit that it was a separate process due to it being a separate system.
Side note: as an ex-IT type person I can't believe they're at least two separate systems. Separate interfaces into a single system, yes, but not separate systems. That wouldn't make sense.