[bob_hackr]

I just did this a couple of days ago. This thread was quite helpful:
http://www.kawiforums.com/ninja-650r-er6/159310-generator-cover-bits.html

You didn't say where you live, pretty much every car/bike store will have something along the lines of 'liquid gasket' (basically just silicone sealant). You could probably get away without the sealant as the rubber grommet should form a decent seal, it doesn't hurt to play it safe though.

If the bike is level, you will lose about a litre of oil. It's probably worth just changing the oil and filter at the same time, unless you've only just done it recently.

When you take it off, watch out for the gears connecting the starter motor to the engine, they will probably stick to the cover. It shouldn't be too much of a problem if you've got the bike on a rear stand though.

As for the bolts, all I did was place them down in the order that they came out. I used the extra long bolt (goes in at about 5 o'clock) as my reference point.

When you go to put the cover back on, I would place a thick piece of plastic between the generator and the cover. This will stop it flying out of your hands as they come together (it happened to me, luckily no fingers in between). The piece of plastic should stop anything getting damaged and let you line them up easily.

These might come in useful