Know this may sound strange but pull the TCU and inspect everything again.

 

OK, I could do that - but I had looked at it pretty good before. Two things concern me... Would the leakage from the capacitor damage the board? I'm including a close up where it seems the leakage crossed part of the printed circuit. Wonder if it's beyond repair? I'm also including pix of capacitors I replaced. Two of them are bad. The other I figured I'd change while I was at it.
The other thing I'm worried about is that the guy who fixed it was not careful handling it - he had his hands all over the printed circuits. I had always understood you only handle by edges and asked him. He said as long as board wasn't grounded it's OK, and they always handle boards w/o problems. Now how do I know if more damage was done?!?
One thing I failed to inspect was the backside... first guy I asked to repair said he doesn't work on "dual printed boards" Maybe there's damage there.
Will upload images if anything looks weird...

 

Where I'm going with this is a FAR REACH but it has happend before, see post #13:

TCU, board problem, Tranny - Honda-Tech

 

I am still wondering about that connection. I had posted a pic of it in my first post, and including again. Thing is, when I look into the connector, the metal contacts seem to be fine... The black "soot" on them is more of a stain on the plastic - it doesn't wipe off. I also noticed the same stain on the IAC connector a few days ago, so I thought it was just normal. Really haven't seen any corroded metal, but maybe I should try bypassing the connector?
The connector in question is for the shift solenoids - the lock up doesn't show any discoloration, so maybe it's not that far of a reach?
Thanks

 

Yea.....you might want to "de-pin" the connector - release the wires from it from the back side and inspect......you could go to a "pick and pull" yard and get a couple - should be cheap and practice on them. You will want to inspect both sides....heck now that I think about it, you can buy a new connector - male and female side. Just need a weatherproof connector with the proper number of wires.

Again, check the TCU. It could have burned the new items

 

Might be too early to yell EUREKA!!!! ....as I've read many posts where people thought they had fixed it then the problem returns, so I'm just crossing my fingers for now.
Before I read your last post, I took your former advise to look into the connector. I did look at the backs and they looked kinda grimey, and I would have de-pinned them like you just suggested, but I don't know how to do that. Instead I got some quick splice connectors and bypassed the whole thing. Disconnected battery for a bit, test drove it and it work great for about 95% of the time. (by the way, the D4 light came on for just a second when I turned the key. It had never really turned off immediately after starting before this) Got home and changed the ATF with the (real, expensive) Honda stuff. The generic ATF I used before looked clean and red, and the plug had just a little bit of sludge, but no visible metal, although the level was slightly higher than the crossmarks.
Anyway, I have since driven the car several times and it's working perfectly through every gear whether I shift it manually or not. I plan to look into the TCU again, as the D4 light is still coming on momentarily but for now I sorta want to savor Third and Fourth gears... I also want to see if any codes appear now that the TCU seems to be working better.
Could you tell me how to de-pin the connectors anyway? I wouldn't mind looking to see just how bad they are inside.
Really appreciate all the help you've given.

 

There are a few different styles of connectors on these, right now I can't remember how those are set up. Some of the plastic ones "un-clamp"/open up. Some relaese from the wire side, some from the connector side.......

Honda OE trans fluid is going for at most $7.99 retail (last time I checked?), by the case you should be able to get a bit of a break????

The D4 and CEL are suppose to come on for ~3 seconds when the key is turned to On/Pos II - this is a "check" of a few things.

I'm hoping for the best for you....keep us updated.