Yes, I'm pretty sure no matter which reed valve system you choose, you will have to lower your main jet, one size. With the V-Force reed valve, you have to cut off the "wings" that are attached to the rubber air boot between the carb and the reed block. Once you do this, you can't reverse back to the stock system, unless you buy the new rubber piece. I'm not sure if you have to do this on the Boyesen or not, but I would assume so. Then again, I don't know why'd you want to go back to stock either.
I don't know anything specific about the CR125, but as a general observation:
(1) Boyesen "tunes up" and has a harder hit;
(2) V Force offers broader powerband and about the same horsepower;
(3) You're gonna have to rejet for either one.
IMO, nothing scientific, but I've run both and I think that's a general overview.
Ive tested both the v-force and the boyesen on the 03cr125. The boyesen was better than the v-force and stock was better than both of them. Don't waste your money, move on to another mod! The DEP pipe is excellent for a mid to top gain, the Pro Circuit is good for a stock like powerband with a little more top. Run short silencers on either pipe. Good luck!