I may have spoken too soon. Driving around the block seems to flatten the battery, and a voltage check shows battery voltage lower with the engine running at high speed (12.4V) than when the motor is shut off (13.6). The book says I should be seeing 14-15V with the engine spinning in the upper rpm ranges.
Repeating the input voltage check with the original voltage regulator in the circuit gives the exact same results so it looks like I don't actually need the replacement unit and I can put the original one back into service which will get rid of the kluged up installation job
A resistance check on the stator wires gives readings way off what they are supposed to be and the recommended solution is to replace the stator. These things range from $30 brand new to $120 used on e-Bay so I'm thinking $30-$50 including gasket or pull mine over the weekend and see if the local salvage yard can help me. The part looks to be common across several models, but that wouldn't be the first time someone had told me that in error.
The backup thing to do is to visit the local Yamaha dealership and confirm that the part is in fact common. They also have a way of confirming my suspicions that XV535 bikes are made mostly from unobtanium by NASA contractors using space-certified parts.