Assuming it's the wrong master in there and the rod is in fact shorter: They put it to the end of its adjustment and when that didn't work (and the pedal assy & slave being fine) the only thing left to do was dig deeper and pull the trans.

You are definitely between a rock and a hard place here, since CT will probably only want to re-do their work and the shop you're at now has their own ideas of how to get it working again.

I think you should try to get CT to refund your money and you just bring the incorrect master back to them.
Explain how their incompetence has got your car ripped apart at another shop and it's costing you more money even after the refund.

Have the current shop put it all back together with the refurb clutch & new fork/pivot. If the shop learns that the master was wrong, it might become obvious to them that is all that's needed to get it working again. A little peace of mind but don't expect a guarantee seeing as your car is "interesting".

Good luck!