I assume if you are doing a full rebuild that the complete assembly will be balanced? Get the balance shaft out of there and it is one less thing to chew up power. There are many debates on this but one thing is for sure, if the engine is bein machined to balance, the balance shaft will certainly be obsolete.
BTW, the balance shaft isn't actually measured and weighted to suit each engine it goes into with the aim of perfect engine balance, they are a mass produced device that is there to add more reciprocating mass to absorb harmonic vibration and internal engine resonance in the mid rev range.
YT sells some stuff to help with the removal of the shaft