Going with kick only you can run a smaller battery, some use one about the size of a pack of cigarettes. It is a .8 amp/hour battery but it serves the purpose. I wouldn't go that small, I might look for some thing in a 4 amp/hour. Search this site for smaller batteries will help there.
On a TCI box you need one from an 80 up XS650. They can be found on Ebay, but they may or may not be good. A bit of a crap shoot.
At this point I might use the Pamco ignition. It may cost a bit more now but will save you later. It has a warranty that is the best in the world, and the guy who designed it is a member on this site. His customer support is the best.
Mike's doesn't list the newest version yet. The one with the electronic advancer, but it is availible from Pamcoptete's ignition website,
www.yamahaxs650.com
I would get the ignition with the e-advancer from Pete and the rest from Mike's Look at his kits. Then buy the parts you need that don't come from Pete. The Ultimate coil and advance rod, plug wires, caps and such.
I wouldn't buy the Iridium plugs from him. If you want them you can get them cheaper at Advanced Auto, around $7 each instead of the $10 each Mike's charges. I like the Auto Lite AP63 plugs. cost around $5 a set from Wal Mart. Run well and much cheaper than the iridiums.
On the reg/rec one from an 80 ups 650 will work. Most of the Yamaha's from then use the same reg/rec. If your not sure check the parts fiche at a place like boats.net to check the bike the reg/rec came from, if it uses brushes, or a feild coil it will work.
I know the Seca's and Maxims used the same reg/rec.
I use a regulator from a 75 Dodge Dart. Was $13 when i got it. About $7 dollars worth of parts from Radio Shack to build a rectifier.
A search of the site will find the info on how to.
Leo