Help diagnose: 3RZ intermittent rough running issue

1999 4Runner 3RZ automatic transmission. The check engine light (CEL) wasn't coming on, so no diagnostic trouble codes (DTC), except as noted in #2 below. I've looked at various threads trying to figure out the likely culprit(s).

Problem: *** One main thing that I don't understand is why the problem is intermittent instead of being continuous. *** It runs and drives good most of the time but sometimes the engine runs very rough like it's going to quit running. It has mostly happened at stoplights (the idle will go below 500 rpm, and the engine has quit, too) but also while driving (I'll notice the change of the noise from the heater fan going from full blast to down low). It seems that it mostly or only happens after driving for 15 minutes (engine fully warmed up).

Other known problem: Exhaust manifold leak. One of the exhaust manifold female threads stripped when I was finishing replacing the cylinder head gasket, so there's no bolt there. I put on a later 3RZ steel header-type one because I've had a couple of cracked cast iron ones. I figure it's leaking about as bad as the previously cracked ones were.

Things I've messed with:

1. I lucked out and found a throttle body at the pick it yourself junkyard, cleaned it out pretty good with throttle body cleaner, and installed it. I figure this also helps to eliminate the idle air control (IAC) being the issue.

2. I replaced the electrical connector for the engine coolant temperature sensor (ECT; located at the very rear of the cylinder head; taking the hood off made it possible to see and climbing on top of the engine/bay made it possible to remove/replace the electrical connector, ECT sensor, and 'cylinder head rear plate'; I couldn't find a 19 mm or 3/4 inch deep socket that fit over the plastic connector part of the ECT, so I broke off that part of the original one to get it out) by crimp wire-connecting one I got from the junkyard. NOTE: At first I didn't get the connector on the all the way- that's when the CEL came on with P0115 (engine coolant temperature circuit malfunction) and pending P0172 (fuel system too rich) codes. I pushed the connector on all the way, started the engine and the CEL went off (I assume the codes cleared).

2a. I'm glad that #2 happened because it showed me that the running rough issue isn't resulting in a CEL and the two codes. I thought the ECT intermittently going bad was the problem (one thread reply said that overheating can ruin the ECT sensor and another said there was a ~recall), which would mean the engine control unit (ECU; computer) defaulted to something like -40 *F, so the ECU would add fuel making it run way too rich.

3. I haven't done anything with the mass air flow sensor (MAF).

4. I've learned that live data scanning might be very helpful in diagnosing the problem(s). I'm considering buying a Bluetooth 'dongle,' or a cheaper handheld scanner. It looks like Autozone doesn't have a live data scanner available as a loaner tool. I don't know how much it would cost for a shop to do live data scanning to help diagnose it.

4a. Another of our cars with a 3RZ has an ongoing EVAP code that I've tried a similar 'replace with known good and/or used from junkyard parts' strategy. So, getting myself over the hurdles of being able to do my own live data scanning would probably be good.

 

Have you checked the charging system and grounds?

I know it sounds way off base and unrelated, but you still want to verify that your alternator and battery are good, and the grounds are tight.

 

No, but I'll do that. Thanks.

 

I had two batteries checked (cold cranking amps) at Autozone and both failed while in my 4Runner, so they couldn't check the charging system, but neither battery has a starting issue in either car. And my 4Runner hasn't had the battery (alternator not charging) light come on, even when the engine is chugging then quits. I'm thinking that the battery and/or alternator would be showing these signs of going bad, if either were causing the intermittent problem.