Ryan,
I went to Thirdgen expecting a lot of help, but since my electronics are entirely different, all they were able to help me with was grinding/porting. I'm actually not even familiar enough with the TPI ECUs to tell you what tables they have in them. What I am doing applies the same to every engine in principle, assuming that all of the hardware is working and the basic settings are correct.
I don't know how to summarize the whole tuning process in a short post. There is a decent description on the MS website:
http://www.megamanual.com/ms2/tune.htm
You have to calculate estimated tables for VE and spark based on engine equations or get some tables from somebody with a similar setup. Then once you get the fuel correct enough to start the engine, you idle it and start tweaking.
Now what you are saying about the process being iterative is true . However, with datalogging and the WBO2, it's easy to see what the Air/fuel ratio (AFR) was when it was knocking. If you were lean, add fuel there. If you were a little rich already (~13:1), then you have to pull timing back. It would be even easier with knock detection hooked up, but I haven't gotten that far yet.
Basically you start off very easy and slowly build the VE and spark tables towards higher load and higher rpm. You can estimate what the next portion should be based on what you already have running well, and this is what gets you close for WOT. There is an AFR target table, so the correction converges to those AFR values. Getting the spark right is actually a lot harder than fuel.
Of course I can't be *sure* until I get up there that the fuel pump and injectors will keep up. Lean is evil at WOT and high rpm. It's actually really hard to tune all load/speed conditions on public roads. I'm thinking I need to find a really long hill to climb. I basically have about 2/3 of the map dialed in. Everything above 4000 rpm is just calculated. Like I said before my throttle cable will only pull to about 80%, but at lower engine speeds this is really the same thing as 100%. It's at higher rpm that this makes a difference.
I will get some more pictures up later of the other goodies I'm working on to go with this.