1998 protege sat since 2007
 

Well got this off a guy thinking I might bee able to get a cheap daily driver. He said when he parked it it started missing and losing power while driving. He had other vehicles so never did anything with it. Started it a few times but heard the timing might be off so he didn't wan to drive it any more to mess it up. So for I got.
Battery
Spark plugs

Want to know where to start, was going to start taking it apart soon?

Which engine does this one have? I just went through a similar experience with a 1997 model (1.5 L. 5 Speed).

I don't know if you are planning to handle the work yourself, but I would suggest changing the timing belt first. It could easily be the cause of the issues you describe, and even if it isn't it is likely due for replacement anyway due to age.

On the 1.5L I pulled the valve cover off to inspect the timing belt. I was lucky as the belt was in excellent shape and had Napa logos on it to indicate a recent replacement. While I had the cover off I poured a little oil on both cams as it had not been started in a while. I did a full tune up and oil change, and while I had the plugs out I poured a little Seafoam into the cylinders to help loosen the rings. When I was ready to start it for the first time I disconnected the wiring harness from the distributor to prevent it from starting. I turned the engine over while watching the oil light until it went out - hopefully indicating good oil pressure. When I hooked the harness back to the distributor it started with no problems. After it was just a matter of running it up to operating temperature and driving it a few times to let the computer reset itself and everything smoothed out.

One last note - if you replace the timing belt plan on doing the water pump as well.