Hi, may I be a bit late but. I've had a husqvarna sms 125 for four years now and I spend last one studying how to tune it and having max power (and making the project itself). If you can fit a complete wiring and stator from the wr, i would go for that, still have lights nd a decent curve despite i've mountes a htm rotor (pvl style) with no lights as I know enough electric wiring to make a harness from scratch, the curve is very good, instant power.
Cilinder on sms and wre is 2mm lower than a wr/cr so the whole distribution is more every day frindly and doesn't need that much manteinance as their competition sisters. if you raise the cylinder, still the chamber cc and shape is different (i'm not 100 %sure, but i would bet are not the same, as many 2 stroke books ensure the dome is very very critical on how the bike gives power or how much power can develop, easy go is the vhm head, (I haven't mout it but i will).
Critical point do not port the bottom end. The engine of husqvarnas is considered a piece of engineering, and it may seem like the shape it isn't very good is all thought. I did port it and after that i taught with a local prep. used to prep this engines for karting and he told me the bottom end was never touched, i'm about to buy some cranck cases stock.
Exhaust: Scalvini is the one i like the most but fmf, doma racing, bud racing, etc. All very good exhaust sty away from the gianelli and arrow.
Cylinder porting: I woldn't modify its shape but clean fundition defects, and polish the exhaust.
Exhaust valve: as I mentioned before, i got rid of the wiring wirh that the power valve was deleted in Imounted thed the pneumatic from htm racing, despite is a bit expensive for what it is (aprilia rs exhaust valve with a case), totally worth it. I was sick of the problems this valve gave me.
Don't remove the balance shaft, it isn't worth the bike has no comfort, and on the road that vibrations are a bit annoying.
I haven't test it on the dyno, I don't know what to guess on hp, as I decompressed a bit the primary compression and the dome isn't a good shape in my opinion (optimal 11,2 cc3) mine isn't there. And I haven't reced any other husq, in spain aren't very common.
If you have some doubt, you know just text here .hope i helped