This is from HamsMKIV on supraforums. it is for an MKIII, however. It is the best approach I have found. This allows you to use an automatic ECU. For a manual ECU you can do it more directly, but you will have to analyze the TEWD carefully to check all the harness wires and pinouts of the auto vs. manual ECU. The programming code for the auto and manual ECU's are different. THe same program, but it has several branchpoints where the manual and automatic ecu's are treated differently, and not all the code has been analyzed yet, so it is plausible that the performance would be slightly different if you use the automatic ECU. Since you have a manual ECU, far and away the best approach would be to swap harnesses and just use a harness for the manual ECU. It has to match the ECU color plugs and preferably the year of the body. IF you have a late 89 body, thats good, because it has all the wiring for any configuration or option that they made that year, so the manual harness should be good. IF you are trying to save money by reusing your harness, it probably is okay, but I haven't seen a paint by numbers recipe for making the harness conversion. It probably is very simple, but I don't want to say without knowing for sure.
anyway, here's the instructions if you keep the automatic ecu and harness:
just completed my 5 speed swap 2 weeks ago. If you have a complete 5 speed parts car you will have everything you need to perform the swap. Here's what you will need:
5 speed.
Flywheel and bolts off of the 5 speed car
lower "wing" tranny mounts that bolt to engine (they are different)
Inspection cover between tranny and engine
Driveshaft from 5speed
Pedal Assemblies
Master Cylinder
The whole swap is really easy. I've never tackled anything like this before and did it in 3 days. I could have done it faster but I was waiting on my clutch assembly so... The only custom work you will have to do is in the tranny tunnel. You MIGHT have to open up the hole for the shifter tower. I opened mine up a little and found out later that I didnt have to. I think it depends on the year model. All the holes are drilled for you to install the pedal assemblies and the master cylinder. One thing I would also recommend is that you have a braided stainless hose made to run from the master to the slave cylinder. The hard line is really hard to get out of the car because it runs underneath other hard brake lines and you wont be able to get it out. You could buy all 3 pieces from Toyota for about $65 or make a new braided stainless hose for about $35.
On to the Wiring:
As for bypassing the neutral safety switch... haha... I feel bad for the many people who have paid someone to bypass this..... I can give you a REALLY easy tip around this.... There's three harness connectors on the Auto... look for the one that is round and has three wires running in it, a BLACK wire, a WHITE wire, and a BLUE wire.... Cut that plug off the tranny with some wire to spare.... Take the WHITE and the BLACK wire and splice them together... Plug that connector into the harness side in the car.... Your ECT ECU will now think your car is in park all the time and it will start right up. Too easy.
You can then wire the clutch switch in line to the ignition wire that runs to the starter relay. It's a white wire coming off the ignition switch. You will only need to do this if you want to have a clutch safety switch, as it isn't necessary. Too easy there too.
The reverse lights I haven't gotten around to hooking up yet.... I will tell you that the harnesses are different between the auto and manual, but the wire colors (RED WIRE & YELLOW WIRE) are the same. therefore, get the male end of the harness off of the donor car and then splice into the male end of your car and you'll be in business. One of the 3 round plugs on the car side have the red and yellow wires to splice into. The manual reverse light harness is a TWO plug harness with a RED wire and a YELLOW wire.
The last one that you need to be concerned over is the Speed Sensor. It's a Rectangular plugged harness with 4 or 6 wires I forget. Anyways, they are identical between the manual and auto, so the manual harness will plug right in. This will enable your cruise control to work. The other wire you have to worry about for cruise to enable is the switch on the top of the clutch pedal itself. It opens the cruise circuit and disables cruise when you press the clutch in... I never hooked mine up because I have an aftermarket wheel and pulled my cruise module out. I will investigate further and get you an answer on that too.
That's really about it. Everything aside from the possible cutting is a bolt on afair....
Oh yeah, one thing I had to do... The hole in the back of the crank for the pilot bearing seemed to be a little to small for the pilot bearing to go all the way in... I used my dremel and sanded it open a tad bit to make a snug fit. That pilot bearing should be fully seated into the back of the crank if it's installed properly. You'll see what I mean when you get up in there.
That should be about it.... PM me if you have any questions or if I missed anything. You'll honestly be suprised at how easy it is.
Good Luck