Thanks for the comments on the Nishiki. To answer some questions, the saddle was replaced with a Brooks C-17 Special that matches the look of the bike and is more comfortable than the original saddle it came with. I'll hold on to the Fujita seat in case I ever want to go back to the factory specification.
The crankset and gearing is also original, so I'm keeping it since the terrain around here isn't hilly enough to require a wider range.
I've settled on 700x28 Panaracer Agilest tires for all my vintage bikes, even though the Nishiki could handle a 32 or more easily. The 28s provide enough cushion and road feel while still looking like they came with the bike. They do well with 95 rear 90 front air pressure.