My brothers 91 Laser does the same thing with the idle sometimes, we haven't changed the ECU yet but we suspect thats the problem.
As for your other problem with the car dying when you turn on the AC/heat, well thats kind of weird. I know when you replace the ECU, your suppose to match up the features that are on your car with the features on the new ECU (ie; 5spd, auto, turbo, PWR locks, PWR windows, PWR steering, etc.) or else some of your features will not work if the new ECU comes from a car without them. But I've never seen a DSM that didn't have AC/heat.
I'd say if you didn't have these problems before you put the new ECU in, then I would change it out. Put the old ECU back in to see if the problem continues, if it doesn't then you know its the ECU.