I have one on my 99 YZ125 and I personally did not feel it made that much if any change from the stock cage and carbon tech carbon fiber reeds. The single best mod I made was the FMF Fatty pipe I thought it lived-up my powerband nicely!
I had the same problem with my 98 YZ125 after I installed an FMF Fatty pipe and silencer, FMF Rad valve reed cage, and FMF torque reeds.
I live in Kansas City (lots of humidity) and I run a stock main jet with a size 40 pilot(one size smaller than stock =leaner down low) with the needle clip on 2nd one from the top. Changing the pilot to a 40 and moving the needle clip up 1 to the 2nd clip solved all my problems. I believe the 98 and 99 have the same Kehin VMX carb so this should be a good starting point for you guys to try out.
Just make sure to ride it around for just a few minutes after any jetting changes and pull the plug and if it is a white color like it is running really hot than you have gone too lean and should richen it back up. A perfect running bike should have a plug that has a nice brown tint color to the resistor with no excess black splooge on the plug. To see a perfect plug check out Eric Gorrs website and he has some pics as well as a nice jetting procedures page.