Transmission Question

I just picked up a 93 Probe SE (same engine as Mazda MX6) with an automatic transmission problem. I was hoping I could fix it up quick, but...

The car wasn't making it out of first gear and was making whirling sound. Anyway, I dumped and drained the fluid and replaced the filter. The fluid was a bit burnt (ok, more than a bit) and was almost half empty. Once bolted back together the car drove much better and the sound was gone, but after 2nd gear it just released. Anyone have a thought?

This is the first time I have ever changed a transmission filter, so I am unclear on what I am to look for in the bottom of the pan. If I am to look for pieces of metal, I'm ok, but there was an inordinate amount of metal sludge the consistancy of rock polishing grit accumulated around the magnets.

Is the tranny worth saving or should I find another?

Find another.
We (Family Business) had a customer with a Golf, whose cam seized in the head. Anyway, after we replaced the head, about a week later the tranny gave out on it (not a happy customer). Anyway, after we drained the tranny fluid out of the old tranny, there was a LOT of metal particles in suspension in the oil. What it was, was metal from the clutches (!).
So...
After my rambling, my suggestion would be to start looking for a new tranny, because this one's toasted.

Will I have to pull the engine to replace the tranny? This front wheel drive car almost looks like the transmission is mounted beside the engine as apposed to tucked under it. Would replacing the clutches (or rebuilding it if I take it that far) be something I should undertake? I've rebuilt an engine, but I've never done much transmission work before.

Sounds like the pump in the tranny, not creating enough pressure. This causes A. Lack of shifting, and B. Lack of consistent oil supply to some of the internals causing the oil to burn and parts to grind (causing the shavings). One other problem it could be, the transmission has adjustable bands, after time these wear out, but this wouldn't explain the lack of fluid. A transmission usually holds about 14 quarts of fluid, you can only drain about 4 at the most when you switch your filter, you're sure it was half empty? Which route you want to take depends on your buget, if you can get a used transmission that you are certain works you can always go that way. Your best bet is to see if you can't get the thing rebuilt. Prob have to give a couple of places a call and get a quote. Good luck!

According to the Haynes manual the capacity in the transmission is 6 quarts. I drained roughly 1 to 1.5 quarts from the transmission and the pan screws were finger tight and it looked leaky on one side, so that would be where the loss was. I had to add 4 quarts to fill it up properly. That is why I said half full. I have a parts car with a good tranmission, however it is manual and I am unsure of how well the change over would go.

About the pump, once I had a proper fluid level, The transmission shifted promptly and strong through 2nd gear until it was to hit 3rd and then just dropped out of gear and reved. I was hoping it might be a vacuum issue, but doesn't sound like it from what I have been getting here.

It could be vaccum, I would check all your hoses and make sure, I'm not too familiar with your specific transmission.