Are you going to bung and insert EGT probes into each exhaust pipe? Or, just monitor the outside header temp? While exhaust header temp will change with engine RPM, this change is not instantaneous. There is a time lag for stabilisation, both with mixture changes and RPM changes. Also, as this is an air cooled engine, the inner cylinders will have a slightly higher exhaust temp due to the added heat of the outer cylinders. How much of an offset between these will you add to determine proper mixture delivery? You're also going to have a fan blowing on the engine during synchronization. You gonna instrument the airflow to each header, as well, to calculate cooling effects?
At idle, the temps will be effected by the Idle Air Screws as well as the slide positions. Better have them optimized beforehand.
Theoretically, if each of your cylinders have exactly the same volumetric efficiency, they will each outlet the same exhaust temp if:
1) The cam lobe lift and duration are identical for each cylinder
2) The rocker lash is identical for each cylinder.
3) Each carb is producing the same mixture for equivalent slide openings.
# 1 is very much unlikely to be true unless the cam has been blueprinted. Every used Honda 550 cam I've measured has had unequal height lobes. Close but unequal, nonetheless. I don't think close tolerances for this part were a priority for Honda. I wouldn't expect the lobe ramps controlled valve timing to be precision, either.
I think the carb sync term is, in reality, a misnomer. The true goal is to get all the cylinders to fire with equal power pulses. If slide one has to be a fraction larger than slide two for them fire evenly then so be it. Having equal vacuum indicates that each cylinder is drawing equal gulps of air and therefore should produce even power pulses, assuming good general cylinder mechanical health and carburetors that behave identical to each other.
Just some thoughts...
Cheers,