I just did this a few weeks ago, and here's what I remember:
1.Make sure you keep the fluid container full at all times, or you'll suck air back into the system.
2.Remove the cap from the clutch fluid res., as well as the rubber diaphram. Fill up with brake fluid from a new, unopened container.
You'll need to get a quick disconnect tool to remove the transmission line from the tranny. I got one at O'reilly's for about $3. I imagine you've already got this if you had the tranny out.....
3. Disconnect the tranny line from the transmission by pushing the tool in on the white collar while tugging on the line to pull it out.
4. Use a screwdriver to press in the coupler on the male end of the tranny line. As soon as you do this, have your help slowly push the clutch pedal all the way to the floor. As as the pedal is at the floor, let the coupler close and have your helper release the pedal.IMPORTANT: DO NOT PUSH THE PEDAL IN WHILE THE TRANNY LINE IS DISCONNECTED AND THE COUPLER IS CLOSED, OR YOU'LL JACK YOUR MASTER CYL.
5. Repeat this procedure three or four times, checking the fluid level in the res. after each pass. Reconnect the line to the tranny, and pump the pedal 10-20 times. Make sure the res. is full.
6. Put a clear piece of hose(I think I used 5/8) on the bleeder valve on the transmission. Use a wrench(I think it was a 5/16, but I can't remember) to open the bleed valve and have your helper push the pedal to the floor. Watch for bubbles in the clear tube, and as soon as the pedal hits the floor and the fluid flow begins to slow, close the valve. Then have your assistant release the pedal. Pump the pedal 10-20 times.
7. Repeat step 6 about five or six times, or until you see no more bubbles and the clutch pedal feels firm. If it's still squishy, repeat the entire procedure again. I had to go through the whole thing three times.
It takes a long time to get it bleed. Be patient, and expect to go through a quart of brake fluid. The good thing is by the time you're done you should have completely flushed all the nasty old brake fluid out of the system. Be sure to pump the hell out the clutch between times when you open the bleeder screw. You may need to repeat the procedure again a few weeks later to get the last bit out.
I hope i didn't forget anything...
Good luck!
Brian