Saturn 98 SL2 check engine light on. Car cuts out

It's an EGR valve code.
Here is a super-good list of every fault code for your car -
https://www.engine-light-help.com/saturn-check-engine-light.html

Have you checked whether it is on model?,does your vehicle can communicate with the variable sensors of the new engine? are the crank and cam shaft sensors the same on serial number or are different? Does the injection system gets the correct fuel pressure or is not sufficient.

check vacuum hoses, pcv valve etc. it seem this is not electrical related, it is more of air exchange if my term is correct, example is the hose from engine to air filter and so on check everything cuts,kinks, rubber tend to crack at age, or when soaked in oil this sort of thing.

Check to see if your catalit converter is pluged up

Not to scare or offend you but it could be many many things. It does help that the check engine light is on, though.
If you can go to a place like Autozone, where they check your check engine light for free, and post what the code was, I can give you a place to start.
I do not mind helping you further with a proper diagnosis procedure either, if you can share your vehicle information.

Sounds like a MAF(Mass air flow sensor, you can start by pulling it out, it's inside the intake box on this car. You can clean it with a high percentage isopropl alcohal or MAF cleaner, this sounds to be the problem, if it is really bad, you can unplug it temporarily, it will not have as much power but it will run better. If cleaning it doesn't fix it, then you will need to replace it, ensure not to touch the sensor itself at all.

sl1 has single overhead cam sl2 has doubleoverhead cam

the check engine light means that a code has been set. the code will reference a faulty system that must be diagnosed and repaired. sorry for the vagueness, but there are e gads of codes that can cause the rough idling

most aftermarket parts places will scan the car for free. this will give you an idea of where to start.

check all your air lines

traction control is for wet or slippery conditions it can either be turned off or on