I have a V6 99 Honda Accord EX with a problem that seems like the transmission but I don't think it is?

I have a V6 99 Honda Accord EX with a problem that seems like the transmission but I don't think it is?

Added (1). I have a V6 99 Honda Accord, and I got on it a little to get to highway speeds and the cars power kind of died on me and I noticed that my D4 Light was blinking, which is basically my "Transmission Check Light". Not having a transmission code light, I tried using an expensive engine check light which showed that I got too much power entering my shift solenoid. So I assumed it was my alternator. So I took alternator to get it tested and it passed charging test but failed a few others.

Added (2). Then My cars power started to completely die out one night while driving, my radio powered off, my cluster lights dimmed and eventually the car died and wouldn't start until the next morning. Had battery checked and it was fine.
Now when I turn on my car, the D4 light takes longer to start blinking. Now takes 5-6 seconds when previously it was instant.

Added (3). I just changed the Transmission fluid today, it was a fairly dark red fluid, doesn't look like it was changed in a while. I'm going to drive it about 50 miles and change it again. Despite there being multiple screens within the transmission, the magnet didn't have a whole lot of shavings on it.

Right now, I can only use my 2nd, and 3rd gears manually. If i put it into 3rd, it won't use 2nd either.

Honda had problems with transmissions between 98-07. This sounds like the transmission has a problem. Find local shop at ATRA.COM for road test to verify the problem and give you a estimate to repair. If indeed a internal problem and needs a rebuilt it will run in the 2500 dollar range

You have to give us a little more of a description than that?
With transmission problems, I assume it is automatic, because manual transmissions rarely give problems.
And the first thing is always check the ATF. Not just level, but color and smell, looking for darkness or burned smell instead of pink and rosy. Any brown or burning pretty much means it is toast usually. Not much you can do with an automatic that is not working right.
Some do have linkage to accelerator that can be adjusted to determine shift points.
Some have a vacuum modulator to determine shift points, and they have a diaphram that can crack and leak. If the problem is rattle on slow, tight turns, then it is often CV joints.

If it seems like the transmission nine times out of ten it is.

Check your ground wires. Sounds like a short.

Check my updates now ^^

? It seems like the tranny,… BUT YOU DON"T THINK IT IS?