Everything Simon said, plus some....
Rear axle nut is a 46mm.
Depending on what year your swingarm is from, you may or may not need the spacer that sits between the hub and brake rotor. For example, if it's off a VFR 750, then no spacer.
But if it's off a VFR 800, like my 99, then you do need the spacer. I'm pretty pissed about that right now, because I bought a Galfer Wave rotor for the rear, and with the spacer it looks ugly as sin, so called up Galfer, and they say that yes you have to keep the spacer. So looks like I'll either be getting a new spacer machined, or keeping the stock rotor. Anyone need a Galfer Wave rotor for their VFR?
Also, to remove the rear axle, once you've gotten the big fat 46mm nut off, also remove the cotter pin from the torque link that attaches the swingarm to the rear axle (found on right side of bike at bottom of link) and remove the external snap ring and caliper bracket that holds the right half of the axle to the swingarm. Note: Use a good set of snap-ring pliers. It's a very large ring and most snap-ring pliers don't expand enough to get the ring wide enough to come off. For example, the Motion Pro ones I had almost did it, but not quite. Same for "OEM" brand sold at AutoZone, PepBoy's, Checker's, etc. If you end up using a set of needle-nose pliers to do the job, make sure it's a really beefy plier, otherwise you'll bend the tips.
Also, do as Simon said and take the time to have the bearings and seals replaced. Like he pointed out, a lot of these bikes have LOTS of miles on them, and this isn't exactly an item that is normally taken care of during service intervals. In fact, checking my service manual here for when it should be inspected....oh, look at that, it's not listed at all on the maintenance schedule.