OBD II & later

Around 1996, manufacturers began to built controllers that complied to what is called "OBD II" specification. 

When you remove an auto trans, and install a stick trans, (Or want to use a different auto trans or want to use an aftermarket trans control computer) on a computer controlled vehicle, the computer then does not get the responses from the transmission it is expecting. It thinks something is wrong and throws an error code. It will still run. If you want to fix this:

If your vehicle has OBD II, you will be able to have your computer reprogrammed by downloading into it the codes for the stickshift version of your vehicle. It is also possible to purchase an aftermarket programmer (such as the one made by Jet) and reprogram these codes however you want

Older computer controlled applications (OBD I)

Early ECM systems in many cases do not even notice when the trans is gone.  They did not receive signals from the trans, they only sent info to the trans. This was true of a 92 GM TBI system I used in my old Bronco. It is also true of te system in my 94 Grand Cherokee (A518 trans) Later, he info began to go two ways, and the computers would notice the trans was not responding. This break-over year, was roughly 1995. the newer the vehicle is, the more complex the ECM interface is likely to be.

One thing that you might try in order to find out:  Disconnect the wiring harness from the trans. Just unplug them. Then try driving the vehicle. The trans will likely go into some sort of fault drive-home mode, and will not shift normally. That is expected. Don't hot rod. Just drive around. The point to look for: Does the "check engine" light come on? Does the ECM throw any trouble codes? If it does not, then it will not likely care if you pull out the auto trans and put in a stick. If it DOES throw a trouble code, here are the possible solutions I have run across:

1. Replace the computer with he version of the computer used in the same vehicle with a  stick trans. NOTE: Check service manual wiring diagrams: Make sure the ECM connector is wired the same way in both cases.

2. I have heard of persons or firms that can re-burn or "Flash" a computer to program it differently. Or perhaps they can simply change the "chip". I have no specific info on this, only mention it  something that has been mentioned to me.

3. We have seen some people "fool" the computer into thinking the trans is there by putting resistors where the various solenoids and trans sensors were hooked up and where the sensors were. You will need to do some engineering to figure out the values of such resistors: measure the resistance of the solenoid coils and any sensors (any temp sensor will change value as temp changes, so the trans will need to be at operating temp to make that measurement. You can then calculate the value and power ratings of the needed resistors. (Note: The VSS is necessary for ECM operation. You cannot "fool" on this one. You must have a VSS. The VSS in 4WD vehicle is in the Tcase.  in some later vehicles the VSS is on the axles. IF it is on the trans in your vehicle, a compatible VSS will need to be rigged.

4. Ignore the light. Disconnect it, whatever. There are to potential problems with this: The first is that you vehicle will not likely pass any state smog inspection with the computer throwing any error code. Thus this would e a off road only solution. The second issue depends solely on the way the manufacturer programmed the ECM: It may go no into a non optimum "limp home" mode on engine management (such as to run "open loop": not paying attention oxygen sensor input and estimating fuel mixture without using this feedback "loop"). Maybe it does, maybe it does not. This will vary from model to model