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You can check your timing on the scanner. Typically, for an F engine with the 5067/5521 model DS4 IP the timing at warm idle was 8.5 degrees (cam referenced). For the unique high output DS4-5068 IP the timing was around 4.5 degrees. OBDII trucks started going to 11 degrees idle advance. I like 9-10 degrees. With a large turbo, too much advance will cause more black smoke and slightly slower spooling. But 10 degrees feels real nice off the line with the GM turbo or something else that spools very quickly.
Holding the TCC lock on deceleration should not hurt the tranny, it sees much greater load when accelerating, you can unlock it by tapping the brake to coast. A lot of guys have been holding the converter locked for years.
I think 2nd gear is most important to increase, because its an acceleration gear, and can take it out to 50mph or better at WOT depending on your gearing. The converter locks in 3rd which already holds that gear long with a lot of pedal.
I dont have Kojo program to comment on, but I worked with him to develop some of the files for tuning calibration tables. If getting ATT I'd request warm idle advance of 9 degrees (10 for a smaller turbo), warm idle RPM of 650-700rpm for alternator and AC performance at idle. I would request max fuel not come until 2100rpm, and decreased max fueling (lower than stock 600-1200rpm) at earlier RPM. If you have auto tranny take 2nd gear out longer over 50% pedal, because power will be there at high RPMs and you dont want low RPMs when upshifts. I also desensitize the fuel pedal, for less fuel at less than 30% pedal, to acelerate slower. GM likes to give 70% of fuel in first 30% of pedal. Make sure to ask for TCC lock on deceleration (at zero/low pedal), if you want to use "engine braking". I have sent him some of my programming so he knows some stuff I do. If you dont already have it, I'd get GMTDScanTech for being able to monitor engine parameters and set the IP timing.