My Sportmax 002's got some kind of mud or tar/residue on it, so
so I started cleaning them thinking no big deal, and noticed this
clear coat/plastic coating stuff started coming off the wheel.

Good news is I got the nasty grime off, The bad news is that clear
protectant came off on part of the wheel and doesn't have that nice
polished shine to it anymore. I was thinking about clear coating my
wheel, but wasn't sure.

Anybody know how to fix it or get it back to its original state?

 

I would defer that to a wheel repair shop. There are places that recondition damaged wheels. They would know exactly what to do with it to make it right. The problem is the cost will likely be $100-200. How much did the wheel cost?? Perhaps replacement might be a better option than this. You could have the wheel recleared. the problem here is that the polishing of the entire wheel surface must be even or the result after clear will not be. May require removing the rest of the clear on the wheel , polishing and then clearing, again the cost may approach the cost of a new one and even after it is fixed it may not exactly match the rest of the wheels.