'97 LT1 running poorly...

[LT4Hawk9]

Here's the scoop:
-'97 T/A's LT1 installed in a 1980 Scout.
-Stock except for LT4 Hot Cam
-True dual 2.5" exhaust, stock manifolds, with no converters
-K&N conical filter just ahead of the MAF, into stock elbow with silencer removed and blocked off
-Pre-electronic 700r4 from 1990 Blazer
-Accel Opti, about a year old

I had nearly 200k on the stock engine, and it chucked a #8 rod bearing back in April. This was on my way from VA to Charlotte Auto Fair, and I went ahead and drove it easy down and back, parking it when I got home. I ended up getting a reman long block, and am finally getting around to finishing it up. I took the engine, replaced the camshaft and swapped over all of my old parts. Originally, when I put the engine in 2 years ago, I had the transmission and smog stuff removed from the ECM from LT1swap.com. While the Scout was down, I sent the ECM to Ion at MadTuner.com this time to compensate for the cam. I also had him program it for a larger throttle body I had, but it ended up getting used elsewhere before I could get it. So it is running the stock TB, with presumably the ECM programmed for a larger TB. That is really the only funky thing that I can think of with it.


Here's the issue:
I got it running a week or so ago, and it idled great, had great throttle response, etc. All seemed great letting it run for 30-45 seconds sitting in the shop. So I get the radiator all plumbed, fans wired up, power steering plumbed, etc a few nights ago, and let it run long enough to watch for leaks and see if it gets hot, make sure the fans come on, and all that good stuff. So it runs fine for a few minutes, then all of a sudden it starts idling rough. What the heck? I reach under the hood and flip the throttle a little bit and throttle response is SUPER sluggish, and I have to feather it to get the RPMs to come up. If I let it drop back to idle from a 1500-2000 (???) RPM rev, it will sputter and die. Upon trying to restart it, it will turn over, fire a couple times, but not well enough to actually start up. Give it maybe 20% throttle and it will start, though. If I let off the throttle and let it come back to idle on it's own too quickly, it'll die again...or feather it down and it goes to the rough, barely idling state. Now, after a time, ranging from a few seconds to a minute or so, it will go right back to normal. It's immediate from good-to-bad, and from bad-to-good. Like throwing a switch. It's even done it a few times WHILE cranking it back up from dying out, turns over firing and coughing, then all of a sudden it fires right up and runs like it should for a few more minutes.

I am getting two codes, generally two times each. They are:
-P0785, which is for a 3-2 shift solenoid. The transmission is supposed to be programmed out. Ion knows about this and is going to fix it, but I'd like to get the thing running right, or at least diagnosed before sending the ECM back.
-P0336, which is the crankshaft position sensor. I understand that this should NOT effect the performance of the engine. I would like to have it fixed, but I don't know where to go from here, and the performance is obviously more important than the code to me. I put a keyed pulley hub on it from Summit when I put the long block in. The CPS reluctor wheel was keyed, IIRC, so it has to be clocked right, but could I have put it on upside down? The wiring looks okay going to it, and the sensor was working when I pulled the other engine apart, so I assume it's still good. For $150 I doubt I'll replace it "just to see" if it's bad.

Ion says to unhook an O2 sensor to force it to run in open loop and see if it "fixes it". I also plan to put a fuel pressure gauge and timing light on it tonight, to see if it's electrical or fuel related.

Anything else you guys know of to try to diagnose this thing?

[LT4Hawk9]

Update:
I unplugged the O2 sensor and it idles and takes throttle perfectly. Open loop works. I've got a pair of O2 sensors on the way.