Hopefully this thread will contain all you need to know about doing a manual swap on a ZZE110... Contributions welcome.
The Guide:
First, a guide from another forum:
The discussion starts here:
http://trdforums.com/forum/showpost....1&postcount=39
The guide itself:
http://trdforums.com/forum/showthread.php?t=7117
Next, some update to the information there:
You need the C59 tranny. Search doesn't always give you a straight answer. Gear ratio is tall, but IMO with the torquey 1ZZ this combo can offer good fuel economy yet still able to move the car reasonably quickly.
To get a reasonable tranny for a reasonable price, grab the cheapest one from junkyard and send it out for rebuild. The more expensive ones out there may still be crap requiring a rebuild. (Thanks 94_Rolla_Guy for this tip)
TRD Short Shifter can still be ordered from dealerships. As of late May it's C$210.
Don't detach the AC or power steering lines. Unbolt the AC compressor and PS pump from the engine and hang them out of the way. Be warned that setting aside the AC compressor is very tricky, refrigerant loss is likely.
Heavy lifting:
You can use one engine crane to hang the engine/tranny while you unbolt the subframe and crossmembers. When they're free, lift it out.
Electrical:
In my car at least, the wiring for clutch start switch and (if you have cruise control) the cruise control clutch switch are all there. According the factory wiring diagram, to do it right - meaning actually wire up the clutch start switch - you would extract pin 3 (if you have 3-speed auto) or 4 (if you have 4-spd auto) and re-route it to pin 3 of connector IL2 (gray, bottom of the 4 connectors to the right of the center stack). Do this and your car will crank the first time.

Caution: The proper wiring is through the engine wire harness. You need a total of 4ft of wire to complete the routing. A possible shortcut is to abandon the existing wiring and run new wires through the engine room main wire that goes under the left fender.
If your tranny doesn't come with the backup light switch plug, get it from a dealer. Its part number is 90980-11250. There should be no need to cut any wires.
If you have cruise control and want it to work, do it right and get the cruise control clutch switch. This is a second switch on the pedal bracket that opens when you step on the clutch. It takes the place of the pedal height adjustment bolt. The wiring for this circuit is all there and works once you have the switch installed and connected. Luckily I got this switch with the package and didn't have to worry about it.
You should try to get the manual tranny ECU if possible. If you bought your car in Cali then get the Cali ECU, otherwise Fed would do. (This difference is about emissions.) If you're in Canada, see if you can source one from within Canada.

Caution: Beginning MY2000 the 4-speed ECU has a totally different pinout across 4 plugs than the manual ECU across 3 plugs!
The clutch pedal assembly and all the hardware can be ordered from dealer, just that it won't be cheap. Junkyards that use the car-part.com (interchange) system cannot tell you directly if they have the clutch pedal assembly because this is not something that system tracks.
Be prepared to buy a new rear engine mount as well, it may be different between manual and auto.
Insuring and registering the car once you're done, aka red tape:
The company I currently have insurance from wants me to tell them if such a swap has been done, but it claims no difference between manual and auto Corollas. Ask your own insurance company to be sure!
In Ontario, Canada, transmission type is not something the transportation ministry keeps track of, so no need to tell them - they don't even check that during safety inspections, and that doesn't even get done on passenger cars except when changing ownerships

. Your state/province may be different.