Hi,

So we have all injectors operating again, but 1&2 are flooding.
There really isn't much that can cause an issue specifically on 1 and 2 and not 3 and 4.... 1 and 4 or 2 and 3 would be one thing, but that is an odd combination. Really you are limited to ecu, coil, injectors (individually), etc.

I am assuming at this point you are only using the 1G engine and CAS and have transferred over your old coil and injectors. If you haven't, do so now to eliminate any variables there.

Otherwise, make sure you have your CAS wired correctly and that it is not backwards etc. There is an illustration of the wiring HERE, as well as additional support information about 1G into 2G swaps (some head-specific swap information, but lots of details that will translate to your situation as well).

As much as I do not like throwing parts at a car, without knowing the history of the injectors and regulator it may not be a bad idea.

There should not be anything to note about the injector order. Particularly, you are using a 1997 computer and wire harness, so the only variable is the CAS and actual engine hard-parts. Regardless, all inline four cylinders fire in the same order, and this particular engine the injectors are always wired with switched power to all four injectors (shared) and individual ground signal for each injector. As long as there is no modification done to the wire harness, and the correct ecu is used for the wire harness and vice versa, there is no way for the injectors to become backwards or anything of the like.

The only thing I am aware of as far as things being inverted are the cam signal is backwards on early 95 model ecus, so instead of a 5V on 0V off cam signal it is the opposite. Even if this were the case, it would not prohibit the engine from running relatively normally, it would just be a little less smooth and more likely to stumble under hard acceleration.