2000 cherokee engine light came on. Put it on a scanner and cylinders 1&3 have a misfire. Where do I start. Checked spark plugs but they look new. Now what?

 

How was the spark on those plugs? What color? that actually has a lot to do with it I'm pretty sure.

 

Has it overheated anytime in the past?

You could swap some wires and injectors to rule those out. I can't remember if the 200 has a distributer, but if it does. You can remove and clean the contacts.

After that i would do a compression test, it will tell you a lot, let us know the results. If the compression is bad, I would do a leak down test.

Also in the mean time you could drain a little of you coolant into a bucket, let it sit for an hour or so, then look for an oil slick on top.

Has it overheated anytime in the past?

 

2000 does not have a distributor. It has 3 coil packs. Could be a lot of things. Cam sensor, dirty injector, bad coil, loss of compression ect ect. Pull the plugs and see if it gives any information. Does it run bad?