Your problem is not the engine because those two engines are almost exactly the same. I think one may have a slightly bigger bore, but it's such a small difference you would never feel it. The difference in power you are feeling is most likely either in the final drive gearing or your engine is tired. Yes, the 200 engine is a direct replacement, but unless you're replacing yours because it's tired you're wasting your time. The horsepower numbers are probably near identical when both engines are running correctly.
85 Tri-Zinger 60
85 ATC250SX
86 ATC250SX
87 ATC250SX
02 XR650L conversion
84 ATC 480R