Dave - before you do any tests make sure you are using the latest firmware otherwise you will need to repeat the tests.
Good luck finding problems - you are likely to struggle!
Black dots - in the year I've had my 5DII I've only ever spotted them on only one image by taking pixel peeping to extreme levels. That was with the firmware update that was supposed to fix it. It will never cause you a problem.
Vertical Banding - I have seen this at ISO 100 when I fluffed my exposure and tried pulling the shadows in PP by over 4 stops. Still wasn't stupidly bad but did have banding. If you take the shot even approximately right you will never suffer from this. High ISO is a different matter H2 cannot be pulled without lots of banding, H1 is a lot better and 6400 is wonderful. I know I can take an image at 6400 and print at A3 with no noise reduction and the print will look superb.
Hot Pixels - it's weird but Lightroom shows a few hot pixels in the low quality image displayed before it fully loads the rest of the RAW file, then they vanish as soon as it finishes loading. Like Robert I have never seen a hot pixel in a production image. I read hot pixels can more easily be spotted in high ISO video, I tried but failed to spot any.
Err 99 - I had that. I think it was dirt on the lens contacts as cleaning then with my lens cloth sorted it out. My 20D used to get that with the same lens - same fix too.
I've had one weirdo where the camera locked up on me. Even turning it off and on didn't fix it. Battery out for a minute sorted it out.
Long exposures (15min+) and Live View eat batteries. I twice managed to flatten a fully charged battery in a single day. I eventually managed to find a source for a second battery; they were unobtainable for a LONG time.
IIRC your old 5D metering is similar to my old 20D. I believe the evaluative metering changed significantly on the 40D onwards - you will notice! I gave up guessing whether the evaluative metering would get it right and now use center weighted metering.
I was initially very disappointed by the 5DII. It was better than the 20D but wasn't producing the jaw dropping image quality I was hoping for, just a lot more pixels. After a lot of navel gazing I found the problem - my technique. To get the best image quality you have to be a HUGE perfectionist but when you get it right by god it delivers. Producing an A0 print you can walk right up to 10 inches away from and still feel you aren't seeing all the detail is an amazing thing. But it took a huge learning curve to get that image and you should not expect it from day one.
