MaximRecoil has good, strong reasons why TR47 should be included as part of the name. I think he's right that both Cowclops and TR47 should be mentioned. Something like "TR47 presents Cowclops v.2" or "TR47 v.2 powered by Cowclops" or whatever. It's bound to be a bit clunky, but what can you do?
Thrashing out the details now, before the set is released, is far better than the alternatives. As long as Cowclops is given his due, MaximRecoil is right to be further thinking of 'branding' and continuity.