If the bike runs lean at top RPM after the new parts are installed you will want to jet upwards. Of course it may run lean at mid throttle and a different needle might be called for too.
Some carbs may already be fitted with a main jet that can handle it.. The stock Honda/Keihin PA50 II carburetor has a #78 jet and an expansion chamber did not make my engine run lean.. it was just about perfect.
Bottom line is to carefully test your new setup with properly done plug chops at various RPMs and riding conditions.. Sometimes periods of leanness are unavoidable and other measures should be taken to protect the engine, like using more oil in the mix.
If you desire top performance some of these tests might show some dangerous leanness but thats the price you pay if you want maximum power.. The edge of too lean is where max-power is.