After I did my 3.4 sawap in my trooper, I was having the same problems you are having, crazy surging after warmup at idle, and dead spots when accelerating. It was driving me crazy.
I ended up unplugging the IAC valve, and all my problems disappeared. I tried putting in a new one, and the problem came back when I plugged it in, so I just left it unplugged.
It's been a year now, and it still works.
I don't know if you have an IAC, but it might be worth trying to unplug it. Might be a lame fix, but I've not had any problems.

'91 Trooper
3.4 V6, K&N, 33x12.5 Trxus MT's, Aisin hubs, 3" body lift, Rear ARB Naches Trail