You have a different displacement engine that draws in a different amount of air. Did you replace the mass air flow sensor that matches the engine? What about the Engine Computer and its wiring harness? It is expecting to fire the injectors for a specific period of time. That won't be long enough if you're using the old injectors because a larger engine requires more fuel per revolution. Based on the oxygen sensor readings, the computer can only modify fuel metering by plus or minus about ten percent. If it sees that it has to constantly add fuel to achieve the correct mixture, that alone can set a code.
The computer knows how fast the engine is running. Along with throttle position and air temperature, it can calculate how much air, by weight, should be entering the engine. That is not going to agree with what is reported by the mass air flow sensor. That disagreement can set a code.
A '95 Engine Computer is going to be looking for a different signal from the crankshaft position sensor than a '00 computer so you're going to need the newer one and its wiring harness. Starting with '96 models, there needs to be another oxygen sensor after the catalytic converter to monitor its efficiency. Did you install the '00 exhaust system? The missing O2 sensor will set all kinds of codes in the newer computer.
Many years ago we could get away with changing engine years and sizes when cars had carburetors and distributors. Today fuel and ignition systems change every year. When you factor in how Body Computers, Anti-lock Brake computers, and Air Bag computers interact with the engine systems, it is impossible to make all these modifications without taking those other things into account. There's a reason they ask you the engine size and model year when you buy replacement parts. I doubt you'll ever get it to run right until you put the correct engine in the car.
To add to the misery, every diagnostic fault code has a set of parameters that must be met for it to be set in memory. One of those is that certain other codes must not be there. For example, the computer compares expected air flow based on the throttle position sensor, intake air temperature sensor, and engine speed, to what is reported by the mass air flow sensor. If you have a code stored related to the throttle position sensor, it may never set a code related to the mass air flow sensor because it knows it can't make an accurate comparison. Once you fix the cause of the throttle position sensor code, the computer can do its self-tests and will set a mass air flow sensor code. You can end up chasing these new codes for the rest of the life of the car.
Other things you have to consider is the potential need for a larger radiator, (which might not fit), and stronger front springs if the new engine is heavier. The different weight changes the front-to-rear brake bias that has been designed into the car for a specific engine. The added front weight may cause easy rear wheel lockup under hard braking. Lawyers and insurance claims adjusters smile and wring their hands when they find these kinds of modifications and do-it-yourself repairs. Even though the other guy ran the red light, they are real good at convincing a jury you are partly at fault because those modifications decreased your ability to avoid the crash.
Sorry for the discouraging news but there's just way too many variables and liability issues involved. You're way better off finding the right engine, then we'll have a known engine package to start with.
Saturday, April 9th, 2011 AT 2:20 PM