The idle adjusting screw is there specifically to adjust the idle. I wouldn't consider a factory adjustment to be ghetto. Here's how you adjust the idle speed from the Helms:

http://webpages.charter.net/mrfatbooty/pics/idle_1.jpg
http://webpages.charter.net/mrfatbooty/pics/idle_2.jpg

I honestly think the ECU and the idle are separate issues. You should be able to fix the idle even if the ECU is messed up like that. Idle is essentially controlled by a number of mechanical means.

All of this aside, you could have a bad IACV which would explain the almost dying when you come to a stop. When exactly does each weird thing with the idle happen? Is the motor hot, is it cold, does it do it all the time? We're going to need the whole story before a proper diagnosis can be made.