FYI Yamaha did not change the header to allow access to the filter cover until the 2001 model year.
If you have to pay $1k more for a two-six, I would just get the 400 (all else being equal, the older bike will likely have more hours on it...). They upgraded the crankshaft in ’99, so I might prefer that year.
Other than 26 extra c.c.s in ’00 they also added a plate to the clutch, raised 1st and 2nd gear ratios, shortened the frame 10 mm behind the steering stem, went with a “Yamaha-only” flat CR carb, and I think they also moved the bar mounts forward as well. I know I like the way my ’00 turns better than the 400s, but the stock clutch in the ’00 is a piece of crap (thankfully, you don’t need to use it very often), Yamaha should have just left that alone until they figured this out (which they did for ’01).
As for the bigger piston, IMO it makes a good bit of power difference, and changes the engine’s characteristics. The 400 likes to spin, but the two-six prefers to rip and snort down low, though it will also spin up like the 400. If you like to ride around a gear tall, the two-six is for you. Just replace the clutch with ’01 parts.
Finally, IMO the ’00 forks are better than the ’99 units, they did change some things internally, but it isn’t a big difference.
Hope this helps, but the best advice would probably be to buy the one that looks to be in the best shape for the best price.