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When installing a '95 EPROM ECU (or '96) on car with a non-'95/'96 style cam angle sensor, you have to rearrange the plug wires. You will also want to check the "Use non-95/96 style cam angle sensor" checkbox in the Misc tab of the ECU Config tab (called "Invert CAS" option in the ECU→Miscellaneous dialog in the older V2 application).
When installing a '97 ECU that has been converted to EPROM on a car with a 1g or 2gb cam angle sensor, you would not need check the box to invert the CAS and swap plug wires, as the signals should be the same as the ECU is expecting to see. However, if you are installing it in a car with a '95/'96 cam angle sensor, you do need to check the box to invert the CAS, as well as swap the plug wires.
If you don't know whether you have a '95/'96 style cam angle sensor or not, check the passenger side of the valve cover for an externally mounted cam angle sensor. If one is present, you'll see it installed in the area shown below.
If, as the picture illustrates, you have nothing installed in that location, then you have a '95/'96 cam angle sensor and do *not* want to check the "Use non-95/96 style cam angle sensor" checkbox and you do *not* need to rearrange your plug wires.
Refer to the image below.
The illustration on the left shows the plug wiring order for a stock ECU with stock cam angle sensor (any 2G model year). Note that cylinders 1 and 4 go into one coil and then cylinders 2 and 3 go into the other. If you install a '95/'96 ECU into a car with a non-'95/'96 style cam angle sensor, then the order is reversed. But in either case, the plug wires for cylinders 1 and 4 will go into the one coil. And the plug wires for cylinders 2 and 3 will go into the other. For either given coil, it doesn't matter which terminal is used for which cylinder. It only matters that 1 & 4 go into the *same* coil and then 2 & 3 go into the other.
So, that said, if you are using a '95/'96 ECU in a car with a non-'95/'96 style cam angle sensor, use the ordering on the right. Otherwise, the ordering on the left should be correct.
If you have a Coil-On-Plug system, you need to swap primary ignition wires from the ECU instead of swapping spark plug wires. On a 2G, you would interchange the Black/Blue wire from ECU pin 10 with the Brown/Red wire from ECU pin 23. On a 1G, you would interchange the Yellow wire from ECU pin 54 with the Yellow/Red wire from ECU pin 55. In either case, you can swap the wires either at the ECU or at the under-hood Ignition Power Transistor connector. The wire color remains the same on both ends.
Note that primary-wire swapping described for the COP setup could just as well be used in lieu of swapping plug wires even if you don't have a COP system.