Q: Brand new clutch installed and on the way home it grinds while shifting into 3rd and it never did that before.

Hello. I share your dismay. When a clutch is replaced it does not implicate any of the internal gearing of the transmission. Although it would seem improbable (because you are not experiencing grinding in gears other than 3rd) you might ask them to double check the bleeding and any visible external mechanism (lever) that might give a clue as to whether you are getting full disengagement of the clutch. It’s a long shot but of course the suggestion is prompted by this incredible coincidence.

One possibility I hate to mention is they of course could have somehow damaged the transmission in any pre or post "test drives" (I don’t recommend valet parking). To evaluate that possibility you would have to do a literal forensic examination of the parts involved. This is not impossible by any means but I suppose it will not help you one way or another as you simply need a fully repaired car.

As far as the cost to drop the transmission, get in there, and repair third, it is hard to say without knowing full extent of any hard parts that might be needed. Obviously, removal and rebuild, or removal and limited repair is relatively costly.

At this juncture, if you are keeping the car, an option is to get the shifting issue diagnosed by YourMechanic for a second opinion and perhaps link up with one of their certified transmission specialists who could no doubt get this resolved for you at a reasonable cost.