99 Honda Accord V6 Auto, Electrical or Trasnmission Problem?

Update: 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.
Update 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.
Update 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.

Your question for help is very confusing and not clear. Your Accord has the J30A engine and CG5 four speed automatic transmission. Now let's discuss about the Accord problems:

You've stated: "I tried using an expensive engine check light which showed that I got too much power entering my shift solenoid" What is this? Explain please.

The D4 light is flashing. Dose the D4 flashing all of the time and doesn't matter what gear you're in? What's the code or codes? Do you know how to use the paper clip method to make the check engine light flash and give you the code? There's a plug under the passenger side of the dash jump it out and the check engine light will flash a sequence of flashes and pauses. 99% of the time when your D4 light comes on and the CEL comes on and your speedo drops to zero it's the VSS (Vehicle Speed Sensor). Look at this video, it'll show you how:

I would suspect the transmission had failed shifting solenoids, which one depends on the code(s). So give me the code(s) and we'll discuss further how to fix the darn car. Defected VSS will also affect the car shifting.

Now, about the charging system problem: Since you have both Alternator/ Battery tested out good so there are only two common things to check/test: The Parasitic drain and the ELD (Electric Load Detector)

Now go and test the vehicle out and E mail me, give me your E mail address so I can send you an FSM (Factory Service Manual). You'll need the manual when I discuss about the problems because I'll not explain or telling you how "Stuffs" work. Everything will be in the FSM. HTH

TELL ME WHAT YOU'VE FOUND OUT and YOUR E MAIL