i just got my tranny rebuilt, and so it seems to be shifting fine, but my stalling problem seems to have turned into something much worse.. my engine sound strange accelerating out of 1 and second (partial or wot) and i'm not sure what the sound is, but there are popping random popping sounds and thumping as if someone was hitting the bottom of my car with a bat or something... freeway, engine sound smooths down to normal, and no pops or thumps... can anyone describe briefly the differences between the 3 things in my subject and what they sound like so i can troubleshoot? thanks.

p.s. my ecu was giving me temp sensor voltage and batt voltage errors which i knew to be false, i switched out the ecu and it gave me only an iac error which i am going to try to switch out also... but are these likely to be the problem? plugs seemed clean when i pulled them out couple weeks ago.. but i will probably try changing those too

make sure when they installed the tranny that they tightened the motor mounts/tranny mounts that could be your thumping.

and it sounds like you need to get all the codes pulled and fix each one, sounds like a bunch of bugs need to be worked out.
The IAC motor problem is the cause of your stalling along with the temp sensor

well they replace my mounts too, so those are good, the thump i'm almost certain is misfire/backfire/detonation, i'm just not sure what the differences are... and like i said, i'm pretty sure the computer is fried, and might also be causing my stalling? my car doesn't stall because of low idle speed, when it stalls, its as if battery power was disconnected for a split second, the codes disappear, battery light goes off for about 2-3 seconds and engine just sounds like it misses a beat if i'm on the freeway, (it will give a quick hard shake and come right back on, but if i'm at a light, the cel and batt light go out, then idle drops down quick and slowly recovers back to normal idle. does the iac have an o2 sensor or anything on it? i'm wondering if that could be a problem, or what other sensors are there from throttlebody to end of intake manifold that i should check?

i have had the same misfiring thing somewhat....my problem was the IAC and the ECU tho (ive gone thru three ECUs in two years), but my would sputter, stall, and then after i reset the ecu it would drive fine again for like the next 30 min. and it would misfire like a mofo, with great plugs, good o2 sensors, and everything. then pulled code for IAC, after i replaced it, ran good but still stalled out. finely it quit, had it towed to a dealership, and nothin off the ECU.
so in short of the story, try the IAC first, its held in by two bolts and sticks out by the TB, and if that doesnt work pull some codes, or change out the ecu which is $230 from a dodge dealership new.