Ive got a standard gearbox from an ST150 in my kit which doesnt retain the standard pedal box and master cylinder.
My question is, do I need to restrict the movement of the pedal so that I don't throw the release bearing out too far and do damage?

Yes, you need to find out the bore size of the slave and master cylinders and work out the relevant travel required...

Sounds pretty technical to me!
Cant I just put a stop on the clutch pedal and adjust it so the there is very little movement after the clutch has disengaged?

Yep, if you can see it. But normally you can't....