Can the wrong EEC cause Idle Surge?

I have a odd idle issue ever since I swapped to a 5 speed and I don't know how to resolve it. I idle surge (occasionally but enough to want it to stop) after I come to a stop light from driving. Sometimes it will drop to low idle perfectly, others it will drop straight to dieing, AND sometimes it will drop, almost die, then start surging. If I am just sitting and crack on it, it drops to smooth low idle nearly every time. TPS is at .96, Idle set to 800rpm (when it idles), fuel pressure set to 40 psi with no vac and drops to 38 with, timing set to 10 degrees with the pill out. I checked for vac leaks and none found. Not that I really think it matters, but I got new plugs/ wires/ cap/ rotor, coil, hell even a whole new distributor. Module on the dist. is one I've had for years so I don't know about it. My real question is about the computer. I didn't change from my A9P when I did the swap and I know the timing curves/ fuel maps are a little different. Can the computer be changing the timing to abruptly with no load on the engine causeing it to die? I assume the eec is set to expect a small load on the engine with an auto trans and it adjusts the timing to drop at a different rate. Right or wrong? I've tried doing little experiments by letting the clutch slip some as I slowly come to a complete stop and push in the clutch just as I reach a stand still but I don't quite have it down well enough to prove or disprove my theory on load affecting fast idle drop. BTW, fast idle as I slow down is around 1500 rpm and stays there till I stop and then SLAM down to around 600 which either the car recovers or dies. I've been in factory 5 speed cars and don't remember there being such a harsh drop in rpm as I was stopping. It's aggravating and somewhat embarrassing to be in the middle of town and die at 3 out of 5 stoplights!!! OK, thats the problem; here is the list of mods!!! 351 bored 40 over(357), Trick Flow Street heat intake, AFR185 heads, Comp Cams XE274h cam (230-236 duration 519-523 lift on 110* lobe seperation), 1.7 roller rockers, 24lb inj, 70mm TB, 80mm Mass, 1 5/8" BBK unequal length headers, 2 1/2" off road X-pipe into Flowmaster 40 series cat back (full tailpipes). ANY SUGGESTIONS?!?!

almost sounds like you arent getting enough idle air. probably could fix that with some fine tuning.