1996 Civic EX-R D16Y8 4sp Auto

So this is my wife's car and she is a nurse working graveyard so I haven't been able to convince her to swap manual in it, she ends up very tired after 12hr shifts, so she would like to keep the auto.
Deal is it started feeling underpowered, and then it started to screw up the gear changes. She isn't so mechanically inclined as I am, but she like it and helps out when we fix her car. She just told be a couple weeks ago that the car was moving super slow even when she floored it, and as it started to pick up speed it started to sort of work normally.
I checked the trans fluid, it was at level and didn't initially see any problems with it, but I decided to do an oil change anyway, proly had about 10k km on the oil, but I'd figure it might get it going. To my surprise it was a milkshake (you know, water mixed with it), and before anyone goes off saying its the rad, it isn't, I put a separate oil cooler in the front just for the trans so I could mount a normal manual rad on it, as the one it had was leaking, and I switched my original rad on my Si for an aluminum, and I figured it cools the tranny oil way better than the one passing through hot water.
After the change I also cleaned out the lock-up and shift solenoids, the shift ones (the ones at the bottom) were a bit dirty on the mesh filter but didn't seem clogged, lock up were good.
Initial codes thrown were 41 and 15, which I contributed to the fact it was miss-shifting. After oil change and cleanup I erased the codes, and some time later it threw 8 for a while, then threw 9. which I also reset and they never came back. On the codes table in the manual, it says that for these codes D4 would be blinking, but it has never blinked. D4 stays solid until I jump the connector to pull the codes.
When you put the car in 2 (D2 if you will) it functions as it should and moves along as it should in 2nd gear, D3 and D4 the trans seems to not want to downshift into 1st. To be honest I feel the trans downshifting but can't tell what gear it goes into. As in I don't know if it goes to first and the torque converter is not working, or if it never goes into 1st at all. Once you pick up speed normally it sort of shifts into what I think is second and from then on it works normally, with the exception that shifts, up and down, are done harshly and the engine jolts a bit (to be honest I just found out the the driver side motor mount is broken, the oil filled one) so yes I am going to change that, but the trans has always kind of jolted when making changes, both from a dead stop as well as with speed, although it jolts harder from a dead start.
Fluid is good and level, clean. Might this be a bad torque converter or the shift solenoids?
Any further diagnostics to do or anything to change or check?

 

Your choices are (1) replace the transmission or (2) do 6-8 ATF drain-refill cycles. With engine idling, slowly shift through all gears multiple times between drain-refill cycles.

You need to do many drain-refill cycles because draining the transmission only removes about half of the ATF. This procedure saves many abused Civic transmissions but not all.

Use Honda ATF or Castrol ATF for Imports, which is cheaper than the former when purchased in 5 quart jugs.

Good luck.

D4 codes 8 and 9 are electrical problems. Make sure the connectors are fully seated on the sensors you removed.
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Forgot to mention its on its 4th oil change as of right now, since the 3rd oil change it was no longer milkshake, it came out surprisingly clean and new. Car was rowed through the gears right after changes, as well as driven to stir up the old and new oil for the subsequent changes. I still want to give it more time to see if it gets working, and of course a few more oil changes, but was wondering if anyone had any ideas on what to look for or check, that i could do in the meantime.
As well thank you very much for your feedback.

 

What ATF are you using? When the ATF drain-refill works, it takes more cycles than you would expect. Visual appearance of fluid is not an indicator of when to stop the cycles.

 

I used the Castrol ATF for imports as it was readily available. Like I said, its currently on it's 4th, but still going to do at least 3 more, I hadn't considered that the visual appearance was not an indicator, I simply thought to do it to play it safe and get all of the contaminated oil out.
But I will definitely run this 4th oil change longer before the next, try and get it as mixed with the old one as possible. Do you have a recommended mileage before the next change or any pointers?

Regarding the connectors, I will definitely re-seat them. I didn't pay much attention since after resetting the ECU, they never actually came back, but I will check it daily and see if they do.

 

Slow movement through all gears multiple times with engine idling to mix old and new ATF is sufficient.

If the connectors are fully seated and clean and the connector pins are not damaged, then do the electrical tests described in the service manual for D4 codes 8 and 9.