On my wife's 00 Accord, we had that happen with the AC off. Turn the AC on, and it would stabilize. So, I'd try burping the cooling system, and see IF you have any codes, before doing anything. If it's an IAC valve code, you could try doing a "re-learn", but if that doesn't fix it, then I'd move onto an IAC valve replacement.
As for the plug, glad you found it, and plugging it in fixed it. I like simple fixes.
As for doing the 99 4 cylinder trans, it should be a little easier, due to having more room. Keep in mind everything will be opposite of your V6 car. For it, you'll need to find a 98-99 trans though, due to the 00-02 getting updated electronics inside.

 

As you said, the guy I bought the tranny from said check the coolant. And as you said, running the AC caused some change. But I finally had a CEL and got a TDC 505, as I recall: idle air control valve and replacing it fixed my problem. I had no idea coolant circulated through these components. I have a couple of issues about it (coolant) still: I could only get about 3 qts into the radiator, but I thought when we drain and remove the hoses all of it shoud drain out- I must be mistaken and a couple of qts are in the engine? And of all the parts I removed and replaced to replace the transmission, I lost one, the radiator drain ****. I guess it's a generic model and I can't get any other plug to work, so I rigged one. Works ok but I guess I'll replace the radiator outright, maybe, and I'll ask you this: should I add an extra ATF cooler and inline filter, as I've been told?

 

Honestly, adding both a trans cooler and a filter wouldn't hurt one bit. In fact it should help with trans temps, and that's the thing, hotter trans fluid temps equal shorter life. With the V6, their life span is already short (known to go bad sooner than the 4 cylinder AT trans), so anything you can do to reduce temps helps.

 

Ok, thanks. I have another issue, and don't know if I should start a new thread, so maybe I'll just ask you and you can suggest that if you agree. I solved the 505 code, but failed inspection because a P1706 came up. "Open in the Gear Position Switch".... I'm not surprised, really. But I don't know what to do. As I said at the outset, I thought the nonstarting was due to gear position/gear selector/cable out of adjustment at trans/"neutral start switch" or whatever we call that thing. happy it was just that connector I had missed. But now I'm back to this, and the symptoms are: can't remove the key unless I fiddle with it in P. Moving selector into gear does not always result in the light on the dash indicating the gear I've selected, and it's KIND OF random. And it's incorrect when it does light up, so it might say N when it's actually R, etc...and occasionally P and D1 simultaneously. So, back to what I've attempted, since I already knew of this issue back when I thought it was what was preventing starting: I tried to adjust the "neutral start switch" as indicated in the manual. Then I disconnected and was more deliberate when I reconnected the cable at the transmission. And last night, following the Hayne's manual, I removed the console and tried an adjustment of the gear selector, which involves disconnecting the cable at the selector (passenger's side), pushing the cable by hand into P then back one click into R, and sliding a pin into the hole on the driver's side and then reconnecting the cable. None of these maneuvers changes the "inaccuracy" of the gear indication on the dashboard. For the record, none of this keeps me from driving normally, and I have confirmed that car starts only in P and N, and interlock seems to be normal (can't shift without brake applied). If I didn't have the inspection problem I would ignore this, other than it's slightly irritating.

 

I would not have guessed this. I think I will disconnect the connectors to the gear position switch (what I call the "Neutral start switch" but don't know why), and reconnect them and go ahead and measure this shaft. I've also read a better detailed description of the adjustment in the gear selector in the Honda Service Manual , 14-129 as referenced here (as compared to the Hayne's), so I may repeat that with greater attention to detail when removing and repositioning the cable.

 

Well, well, well...I am surprised, but that did the trick. As Honda said, the gear position switch is a bit finicky. I removed the cover and the switch and measured that shaft. It was slightly narrower than 6.1 mm. I carefully spread the two fingers of the shaft with a screwdriver until it measured 6.1mm, replaced the switch and cover, and voila: gear indicator lights are correct on the dash. I even think the shifting, both selecting a gear and while driving, is a little better (it started out a bit sketchy with this tranny, especially shifting into R). Passed inspection after I cleared the code and drove through one cycle. You know, my instincts told me, when I installed that switch and all the other switches and solenoids (which, by the way, I didn't replace, didn't even clean, just removed from the old tranny and put onto the new one. I wonder how it would perform if they were all new....) not to sqeeze that shaft. The guy that rebuilt it sent it to me in R, shaft vertical, but I wanted to turn in manually to make sure it was in R before I installed the switch. So I used a crescent wrench rather that pliers. Still, I guess I squeezed the fingers together a bit.

 

Congrats on getting to the root of the problem. Sometimes the Factory Service Manual is better in the long run over Haynes, as it's designed for the car.