96 Geo Metro, Whats wrong?

[FedCop]

RE: 1996 Geo Metro 1.0L 3 Cyl

I ran the car a little too long on the timing belt, I should have known better, they break like clock work every 60k miles. I had the engine replaced with a JDM motor (JAP MOTOR) and it just hasn’t run right since. (Brother, back yard mechanic did it) Almost seems like the timing isn’t right. Runs a little rough at idle. Hesitates but then will take off like no tomorrow and then all of a sudden at highway speed it looses power, sputters and such. It soon stops doing that and takes off again. Fuel mileage is not that great.

One additional thing, when the engine was changed out, the timing belt gears (what the belt runs over/around and has teeth on them ) did not match the old engine, so both gears were taken off old engine and put on new engine, could this be the issue? One had square teeth, the other was rounded teeth, and we had a hell of a time finding a belt to fit it. Why we did this I do not recall. (been awhile) Car has been run about 10+ k since engine trade out and has always had an odd whine to it.

The car isn’t worth a whole lot, but I love the great mileage when it is running correctly and driving it saves wear and tear on my gas guzzling 2001 Blazer.

So, tell me whats wrong and what needs tobe done to fix it....please!

Oh yeah, the check engine light is on, I keep looking under the hood, and the engine is still there.... (a joke, a funny that is) I don't know how to determine what code(s) are causing this.