You can try cleaning your idle air control valve and then lube it with WD-40. Check again for vac leaks.
FWIW, when I used T5Suite to reflash my ECU to Stage 3, I had an idle problem afterwards. The car would warm up and then when stopped at a light the idle would go very low (800) and "hunt". It didn't stall for the most part but it would run rough for 5-10 seconds then go normal again and repeat again down the road.
I fixed this problem by reflashing my ECU again, using the original, modified code on the second flash. Idle problem is now gone. On the first flash I used ECU code that came with T5Suite (it matched my ECU s/n) but this code was missing something. On the second flash I downloaded my stock code, modified that and then flashed back to the spare ECU. The main difference in the binaries was the setting for Program Control Flags (Pgm_mod!) found under MISC | ADVANCED. I can't be sure that this exact thing is responsible for idle behavior but I know reflashing helped in my case. One other difference in the flashes was to have PURGE VALVE MY1994 enabled under Trionic Options. This was not checked on the first flash.
This is a lot of extra, marginal info. but someone may find it useful.