This is interesting. I have not had any of the above problems and have had great support from Josh Dankel at Cobb...
I have taken several logs and sent them to Josh and he helped me fix the minor throttle closure issue using AccesstunerRace.
I don't appear to have the rich AFR problem either. Here is a log WOT in 2nd and 3rd gear and my AFR looks great to me. 2nd gear it takes a second to build boost but that is just from low engine load from the low gear.
I haven't gone WOT at 200kph+ (my speed limiter is set at 130mph/210kph) and I havent seen that error you describe so I can't comment on that.
I know this is just a picture of my excel data but you can see my actual load follows requested load very well and my AFR's are not too lean nor too rich.
Hope you get your problems sorted! I feel like there must be something else going on with your car or maybe limited to your ROM version? My ROM is 97V0B and I am running Stage 1 Aggressive with straight 93 Octane.
No problems and I would definitely recommend the AP from my experience.