I ride a 98 ZR 600 EFI Limited Edition model.
I bought it in 1999 with 1400 miles on it. It had just got new pistons and cylinders from the recall. I have ridden it for 6 seasons and plan on riding it for at least one more before I replace it. It now has got over 6500 miles on it. Overall, it has been a great sled to ride, it has enough power and handling is really good. I don't really have any complaints about how it rides.
I have done some work to it over the years though. At 3300 miles, the crank went on it (I think a bearing failed). Replaced: cylinder head, both pistons, PTO side cylinder, stator assy, flywheel key, crank seals, crankshaft (rebuilt), intake flanges, and exhaust gaskets. It was way off warranty, but Arctic Cat paid for: head, one piston assy, cylinder, stator assy, crankshaft. This crank problem was very common on the 98's. Almost all dealers I talked to about it had seen it happen on others too. Another common problem part on these was the stators failing. I haven't had any trouble, but that's probably because mine was replaced when they did the motor. It seems like the 98's are good once the crank and stator have been replaced. Lots of guys are still running them with no problems.
Another thing I have worked on many times is the drive clutch. I always change the cam arm bushings more often than alot of other people. I'm not really sure why, but since it's not that big of a job, I don't really worry about it. I replaced the entire original clutch at 4200 miles and will be replacing that one before I ride this winter because the spider has a crack in it. I'm sure if I would have gone one more mile last spring, it would have flown apart.
As far as just the regular maintinance goes, twice I've disassembled skid frame to check and replace any worn out bearings, shafts, and bushings (3700 & 5500 miles). I replaced original belt @ 4200 miles. Replaced driveshaft bearings @ 5500 miles (they didn't need it but I figured they had enough miles on them). Replaced original sliders @ 5500 miles. One broken front shock @ 5800 miles. I always grease all the fittings all the time and check everything over pretty good. Changed chaincase fluid a few times. Keep everything clean so I can see any problems developing.
Never had any problems with the EFI system at all. It's still working great.
Overall, I don't think I can complain about the quality of this machine. I ride pretty hard and don't really baby it. I wouldn't worry about getting a 98 if the crank and stator have been replaced.
If you have any more questions about these ZR's, I might be able to help you out.