Here's the article as it appeared, pretty much...
Thought I'd better post it in case it ever disappeared. Way useful. Thanks to Ron and the mr2oc!

The conversion is relatively simple if you have a parts car. Just switch over the appropriate parts. If you transfer the wiring harness from the manual car from under the dash back to the ECU, you won't have to do any rewiring for the cruise control or clutch safety switch.

Extra tools to buys in addition to normal hand tools:
Toyota Repair Manual or Haynes manual
10 mm deep socket
12 mm deep socket
14 mm deep socket
30 mm socket ½-inch drive (for axle nuts)
10 mm and 12 mm hydraulic nut wrenches
Drill bit (5/16)
A second hydraulic jack

1. 5-speed transmission (which includes the shift lever on the transmission [selecting bell crank assembly: #3590F & control shift lever: # 33527] and reverse switch: # 84210). You also need clutch release fork: #31240, clutch release bearing assembly: #31230, release fork ball: # 31236, and clutch release fork boot: # 31126.
2. Flywheel (may need resurfacing) (Note the early 1985 MR2s have a smaller diameter flywheel and clutch)
3. Master cylinder assembly: # 31410 (consider purchasing a new one)
4. Slave cylinder assembly: # 31470 (consider purchasing a new one)
5. There are five sections of hydraulic lines from master cylinder to slave cylinder and one section for the slave cylinder bleeder.
A. Hydraulic line from the master cylinder to the 90 degree angle fitting: # 31481
B. 90 degree angle fitting between the "L-shaped" line and the long hydraulic line that's beneath the car: # 31481B
C. Clips between long hydraulic line and the line near the slave cylinder that attach the line to the body
D. Flexible hydraulic line: # 31481A
E. Short hydraulic line between flexible line and slave cylinder: # 31482
F. Hydraulic line for slave cyklinder bleeder: # 31407
6. Transmission control cable/Slave cylinder mounting bracket for shift cables that bolts onto the transmission: # 33823 & 33826A
7. Rear transmission mounting bracket (May be the same used on the auto(?))
8. Left and right drive shafts from a car with manual transmission (the drive shafts on the automatic transmission have a smaller constant velocity joint hub and the bolt pattern of the hub won't fit the manual transmission)
9. Shift lever, knob and mounting bracket
10. Shift lever boot (including the rectangular wire)
11. Shift cables (check for wear)
12. Rubber seal for shift cables through firewall (Grommet: # 33821A, Dust retainer: # 33574F)
13. Brake pedal from manual transmission car
14. Clutch pedal assembly: # 31301, and mounting bracket: # 31305
15. All the nuts, bolts, and clips that held all this stuff together
16. Instrument panel and plastic part around it to get rid of the ECT switch (Although you might want to keep the switch for other purposes) and add the volt meter that's on the M/T car's instrument panel
17. ECU from the same year M/T car (1985 and 1986 are the same. The A/T ECU will work without any problems

1. Clutch pressure plate
2. Clutch disc
3. Throwout bearing
4. Transmission fluid
5. Hydraulic brake fluid
6. Electrical connectors
7. Cotter pins for the drive shafts
8. Rear transmission rubber isolator (Good time to inspect/replace all isolators for wear/tears)

The auto MR2 has almost all the attachment points for the conversion already in place. All you have to drill is three holes to mount the master cylinder and the clutch pedal assembly. Fortunately, one of the two panels that make up the firewall already has the hole punched out for the master cylinder and mounting studs. You just have to drill out the second panel to the same diameter.