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OK well I thought I would start an independant thread that has no attachement to anyone person or system to discuss programming engine management systems. There are several users doing this currently with either electromotive systems, stock systems, Haltec or probably even some megasquirt.
Some of the basic issues that have been discussed in other threads are
[EDIT] to prevent the need to read entire thread I will try to update this first post with accepted numbers. These may change as a general consensus is reached. There will always be differences.

idle A/F ITB 13.5-13.8
idle stock 14.2-14.6
cruise 13.5-14.7
cruise A/F ITB 16-17:1 said to be possible. May require 30+* advanced timing. (not confirmed as of 01-24-09)
WOT 12.5 - 13.1

timing idle 0 to 12 btdc (hot-rod would not start at 0 required 12)
cruise 30* to 40*
WOT 30* btdc at peak torque ramping up from 20*. Some say 24* max for twin plug dyno shows even with twin 30* if engine knocks back off timing and recheck. Power loss past 30*

basic a/f ratios
ignition curves
idle
various fuel enrichments, start, warmup, acceleration, air temp, blend

So to kick this off I will start with the A/F ratios. In searching threads back as far as they go the one thing that appears to fairly consistent is the WOT mixture. It appears that the target is 12.5:1 to make power. Some have strayed from this to as high as 13:1 but the majority still put it at 12.5:1 Now that leaves the entire rest of the fuel curve up for debate. I have seen anywhere from 17:1 at cruise to 13.5:1 . The stock system is going to try and get close to 14.7:1 as this is where the most efficient burning takes place. I have found that I get 14.7:1 and it will idle OK but I get a terrible stumble coming off idle. Now that is with individual throttle bodies. The stock system may handle the transistion much better. You will certainly get better mileage and have less emmissions if you can get the ratio up there. The general concensus I have come to is that for throttle bodies anyhow 13.5:1 appears to be about what is needed for a stable idle with no off idle stall. So now the question becomes where do you transition from 13.5 to 12.5. Well I can tell you don't do it right where you cruise or your system will be hunting all over the place. Right now I have 13.5 as a target from 3500rpm 90 kpa down to the minimum rpm and 25kpa. I also have 13.5 for all rpm ranges below 70 kpa. I then transition directy to 12.5 to fill in the upper rpm/ higher kpa area. I don't think the sudden transistion is the way I want it so will be working to smooth that just a bit. I do have wide band with mixture control turned on so if I happen to hit a spot where I have to hold it and that spot is on a transistion then the system really hunts. Anyhow have to go now.