The current 500R series of Ninja has not changed since 1994. So if you want maximum parts compatibility, go with 1994 or later. You can steal from any model year from that point on.
Average usage on a bike is 3000 miles/year. Thus, if you find a 1998 500R, if it has 21,000 miles on it, that's ok. Miles on a older bike is a good thing. It means the bike is being ridden regularly and more likely being properly maintained. Alarm bells go off when you see something like a 1994 500R with 5000 miles. It may be a good deal but expect work to get it to a point where it will be road worthy. The bike with higher miles and a higher price might be the better bargain in the long run when you factor in what might be needed to make a neglected or unused bike a street ride.
Gear, I recommend a budget of $1000. You can do it on $500 for everything but your options and choices are much more limited. You can easily spend $400 on a pair of riding boots and pants. Good gloves run $50-$120. Helmet, prices vary widely. Fit is critical. Your helmet must fit correct or it is useless. You can get helmets for as little as $60 off a clearance table all the way to $500+ for high-end models. Consider $180-$300 a good range for a lot of choices. As long as the helmet is DOT approved (Snell is good and I never buy a helmet without Snell approval) and it fits, it will work. Jackets run anywhere from $80 (for cheap textile) up to $500+ for race weight leather. Look for CE approved armor. Consider that mesh and textile gear are best considered "one use" items. If they tear or burn through, they're done. Good compromise for average street riding. I personally prefer armored leather for the greater protective factor (three times that of good mesh/textile). Jeans are not protection. Nor are leather work gloves, work boots, etc. These things will shred at anything above a slow crawl. If a five year old child can wear the knees out of their jeans in a summer of playing in the dirt, how well do you think that same fabric will stand up to being dragged across rough asphalt at 45mph? Get gear you'll want to wear all the time, every time, and WEAR it! Get the best you can afford. Bikes can come and go but gear is constant.
Getting a bike roadworthy depends on what is wrong with it. On a used bike more than a couple years old I expect to replace the tires. The tread is either worn down or their are hairline cracks in the sidewalls. That means the tires are shot. Usually an oil/filter change, new tires (if needed) and a brake fluid replacement (for an older machine) and maybe a coolant flush and valve adjustment is all that is needed to get a used bike into tip-top shape. The first two are not uncommon. Get a bike to a good mechanic and have them look it over before buying it. The $50 or so for that inspection could save you hundreds immediately after the purchase if you don't know what to look for.