Don't forget the hammer and the vise grips! Channel Lock pliers are also a good all-rounder.
For a basic motorcycle toolbox I'd recommend the 1/4 drive metric socket set, which hopefully will include a couple extensions, ratchet, flex bar. For smaller areas a 3/8 drive set is very handy, and should have a nut driver handle in it. Deep sockets are great but I really don't think there's anything on a bike that needs them, is there?
A metric combination wrench set is good, if you have some money for it get a metric stubby wrench set. Having two wrenches of the same size can be very useful at times. Most motorcycle fasteners range from 10 to 15mm, I'm not sure about the axle nut though, I use a 15/16 open end wrench on mine, it's pretty big.
The screwdrivers of course, JIS is best and a couple flat blades in various sizes, including a long skinny one.
Pliers - slip jaw, needle nose, vise grip, lineman's, channel lock, maybe diagonal cutters and you're good to go. If you try to rebuild brake cylinders long skinny needle nose pliers can be used to get the retaining clips out. Oh that reminds me you want snap ring pliers too.
Hammers - ball peen, small sledge and a rubber mallet are the biggies.
Allen keys are only needed if you replace existing fasteners with them, engine case screws and intake screws are popular ones to replace.
Small wire and brass brushes are great, and a large wire brush is often useful too. SAVE those old toothbrushes as well, all of them.
When you get into rebuilding that engine though you'll be needing quite a few specialty tools...
That HF tool set looks like a nice starter set that you can build around, but since you have 1k marked for tools take a look at similar Craftsman sets too, they're about $300 and well worth it IMO and still leave you lots of money to fill it out with extras. For $1000 you can basically have any tool you want and a fairly nice box, though I fear once you buy all the specialty and machining tools you'll be over that, but you buy what you need when you need it, not all at once. IMO invest in a good quality basic set, then decide what can be 'economy' and what should be good quality.
Oh a tip, I got this nice box at Home Repo for a good price, about $130 I believe. It's now $98, you might consider JUMPING on it.
http://www.homedepot.com/h_d1/N-5yc1v/R-203420937/h_d2/ProductDisplay?catalogId=10053&langId=-1&keyword=tool+chests&storeId=10051#.UQsr6aWCmSo