Bradley,
Yes, there are a few differences in the Zetec 2.0 4cyl engines. Some of the engines will have VCT stamped on the top cover; this stands for Variable Cam Timing, which replaces the EGR (Exhaust Gas Recirculation) systems. I believe this was done in the 98 and above models for the Zetecs. Also, the 98 and above models have 130 Horsepower at the crankshaft, and the older models have 125 horsepower. You've got a 99, so you definitely have the better deal!
Also, welcome to the CEG! I hope we've answered your question, but if you have anything else you want to know, don't hesitate to ask.
Ron