He's switching to a contemporary Fuji Connoisseur. Shouldn't be JIS anywhere. All parts from the Vitus should be compatible. Only caveat will the the brake calipers' mounting bolts. The 979 came supplied with specific wider flanged bolts to match the bridge at the rear, and sit flush in the aluminum fork. At least that's what Vitus recommended you use instead of the factory supplied ones on the calipers. If you no longer have the originals, you'll need to visit your LBS.
Funny you mentioned the Vitus rear caliper bolt. I can confrm that something is different with the Vitus brake bridge as I did run into something strange with them when building up my Carbone The brake bolts that came with my Spidel calipers were a little smaller in diameter than the rear brake bridge hole. Luckily I had some small diameter aluminum tubing that fit perfectly/exactly between the brake bridge hole and the Spidel brake bolt. Cut one to the exact legnth and slipped it in and everything works back there. Did not have any problems with the front though. The Spidel caliper fit in with the supplied hat shaped washers that came with the brakeset.
He might not have any problems with the calipers on the Fuji as long as he does not carry over any special pieces that made them work on the Vitus with the bigger brake bridge holes.
Chombi