What I was asking was, were the manual transmissions that were already present in the cars used or the xli/gli ones? Because in the amount that you mentioned, its not quite possible to get the xli's transmission since it alone costs around 30k. If the already present transmissions were used, they would have installed adapter plates to mate the transmission to the engine which often doest go well and
produces vibration at certain speeds/rpms.
2E is less powerful compared to the 2nz-fe but the 4efe is more powerful and. 2nzfe lacks a little on the low end torque compared to the 4efe and when used in a heavy car, it would mean that you'll need to keep the rpms higher when accelerating. Basically, there is a misconception that smaller engines are ALWAYS more fuel efficient. Often, bigger engines, due to better power to weight ratio, end up being more fuel efficient than the smaller ones as they dont have to work too hard to pull the weight of the vehicle compared to the smaller engine. As per my experience, when my father's corolla had a 2nz-fe in it (the same one thats in my charade right now) it would give 12-13km/l within city. Once the 1nz-fe was swapped into it, it jump up to around 14-15km/l with ac. That said, if you commute involves ALOT of idling and slow moving, you would be better off with the 2nz-fe.
Yes, the error codes can be drawn from the check engine light. You'll need to short out the TE1 and E1 wires in the ecu or in the DLC if its connected. DLC stands for Data Link Connector which is used to connect the scanner to the car. It is part of the body wiring and needs to be connected when doing a swap. Chances are, it isnt connected by the electrician. Here's what it looks like,