When I saw how the stock afr line wandered on my SERK, I wanted the best harley fuel management system made hence the sert. I have been riding for 32 years and that was one of the leanest running ecm set-ups I have seen on a fuel-injected bike. Didnt want something that piggy-backed on the factory ecm base map. Not familiar with the Thundermax. [highlight]The extent of the pc3 tuning each cyclinder is that you can trim the adjustments made for both cyclinders to vary by upto 5%[/highlight](somewhere around there, I'm sure someone has the exact number) to account for afr variation. 
Kojak,
The information you have on the PC is outdated. While the cylinder trim capability is still there, you can convert any "Basic" map, meaning 1 fuel and timing table, to an "Advanced Map", with 2 fuel tables and 2 ignition tables. This capability is found under the "Tools" menu at the top of the screen.
Using an "Advanced Map" gives the tuner independent control for tuning both cylinders independently.
FYI, Fuel Table 1 is Rear, and Fuel Table 2 is Front. It would be nice if they told you that upfront.
I have never seen a limit, I E you can go over 100% more fuel in any cell, However the only limit is the injector size and the fuel pump size.
I did find out that if you go past 100%, the PC software gives you a "WARNING: Some table values are out of range." error.
Chief