Since making it a "big bore" is not an option I would probably do some porting, mill or change the head (Bud, Harris, Langston, etc.), maybe reed cage and reeds, change the pipe, get timing and jetting perfect, and let her rip.
For the record this is what Harris performance does to their top tier YZ125. I am not affiliated with them, just sharing info.
YZ125 Mod Stage 3 National Package | $3500
The fastest yz125 available, period. Our 125's have won national titles, holeshot mammoth, glen helen, and regionals.
-Porting stage 3
-Custom billet HP head
-Reed cage
-Custom HP piston
-Crankcase coatings
-Case blueprinting and assembly
-Crank super true, welded crank pin
-Superfinished transmission
-Custom programmable ignition and special powerjet carb conversion, carb mods
-Dyno tune and break in