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I'm a bit confused, it may well just be me...

Does the quintarch get a pulse pistol instead of the pulse carbine or as well as?

Is there an easy modelling option to show the upgrade from a pulse carbine to a pulse carbine mk 2?

You could always paint the Mk2 slightly differently.

All models in the squad, including the Quintarch, get both the Pulse Carbine and the Pulse Pistol.

I converted one of my Quintarchs to have an extra long gun for the Mark 2 (see my thread in this forum), but giving it a slightly different paint job would work as well.

Presumably this is also true for the contractors?

Yes, both the contractors and the team leader have both an assault rifle and a pistol.