Okay to all those 1998-2003 Ford ZX2 5 speed owners, I finally have a complete answer to solve the issue with our cars grinding 2nd-3rd. It turns out that the bushings in our shift linkage wear out over the years and cause the gears to “miss align” when we are shifting. So where do we get the parts you ask? Well I hate to say it but you have to go through ford. There are no two ways around it. Now the part number you will be looking for, for the bushings that you can actually replace is 7A133. If your parts person looks at ya like a moron, tell them the part number has recently been changed. Also if replacing the two vertical bushings does not work you will need to buy a whole new shift linkage which runs around 380-400 USD. Also beware our cars are becoming real pains to get parts for because ford is stopping the production for parts for our cars.
So in closing I hope that since I have done all the back work for you, that this will make your life alot easier. And also a trick to getting those vertical bushings in is to take off the rod next to the shift rod itself. Dont worry any back yard mechanic can do this. Its not hard at all.
-Nick