Thanks and thanks for the pics they should help a lot too.Working from memory, you'll need a few vacuum caps and a block off plate for the head.
The vacuum caps can be those rubber Dornan ones you find at the auto parts store, but I have found that they rot and can leak and that plastic screw protectors work better. You can find the screw protectors at Lowes or ACE.
The places that need blocking off are: one at the vacuum tee on the carburetor, one at the rear of the tank, and one large one at the elbow that goes into the air box under the seat. The first two are small, perhaps 3mm, while the one under the seat is large. The hose is cemented into the elbow but can be pulled out quite easily. The best way to block it off is to take a vacuum cap and shove it in there backwards. I think it is about 8mm.
The block off plate is easy to make with a hacksaw, file, and drill from a bit of 1/2" x 1/8" bar stock from Lowes. They are also available commercially. you'll want to salvage the o-ring from the air injection pipe to put back on the head before securing the blocking plate.
After that it's just a matter of undoing bolts and removing all the stuff and putting it away in a safe place in case you need it later (or, in my case, to continue my reign as the poster boy for hoarding KLR Krap).
I may have some pictures around that will help illustrate; I'll see what I can find and add later.