The 01 port timing allows it to rev a bit higher than the 99. All things being equal, the 01 produces a tad more PEAK HP. With higher RPM, within a given period of time it is pumping and burning more air and fuel, therefore creating more power.
Keep in mind there is no rev limiter per se on this motor – its peak RPM is determined by port timing.
There is a rev limiter on the CR125 and its not the port timing. It’s the ignition curve. The advance drops off a cliff to make for a crude rev limiter of sorts. Run a stock ’01 cylinder with a mod ignition and you will see what I mean.
Very broadly speaking: The ’01 setup is (usually) faster, a little harder to drive (peakier), more expensive to purchase (in kart race-ready form) and more prone to detonation when compared to the ’99.
The PV plugs are essentially part of the cylinder in an ’01. If you junk an 01 cylinder (much easier to do than with a ’99) you have to junk the valve plugs too. ’99 you can usually move your plugs from one cylinder to another if you melt it down.
Running a higher octane fuel like VP C12 (rather than MS-98) helps with the detonation on the 01’s but you may not be able to run that.