I recently fixed a really screwed up 200k mile trans (nearly identical to yours) in a 99 Accord I bought, so I have a bit of insight for you. If you have a check engine light on OR the D light has ever flashed while driving, you need to look at it with a scan tool that can specifically go into the trans computer and see what codes are set. A basic scan tool will not tell you everything even if the CEL is on and there is a trans code you can see with it.
The other first thing to is change the fluid using Honda ATF-DW1. The trans has a drain plug like the engine, you pull it, 3 quarts come out, put it back in and add 3 quarts thru the dipstick hole. You can do that just once, but to do a full service do it twice. Between the 1st and 2nd fluid changes, drive the car briefly on the road or up on a lift. I wouldn’t want to do it with the front up on jackstands unless they are big sturdy ones suitable for a truck and on solid pavement or cement.
So anyway, you will want to use something like a pasta strainer lined with a clean rag to hold over the drain pan so all the fluid goes thru it and it catches any solids. You will want to look carefully to see if any metal came out, and how much blackish clutch dust there is too. There will always be some dust (especially on the drain plug magnet), as clutches are always wearing down. Anyway take a couple pictures of whats there and post them up here if you’re not sure what to think of what’s there. Your ATF can never be too new.
The other thing you can look at is the gaskets for the exterior solenoids. They have fine screens integrated into them to prevent debris from entering the solenoids, so if you have excessive debris in the trans it will also show up here. The dual solenoid looking you right in the face is the best place to start. But make sure you bend the cooler pipes out of the way a little so you can get straight on the 3 little bolts holding it on. DO NOT get careless here and cross thread these bolts. My Accord’s previous owner had done this and I had to use thread repair inserts to fix the holes when I overhauled the trans.
As for the exhaust smoke, please clarify if you are lifting off the gas pedal for the shift change or holding it full throttle during the shift