Add in another KLR owner (well, former, found it wasn't getting much seat time moving from CO to GA... no good off-roading down here near me). Personally, I wouldn't paint it either (it is an instant depreciation in value, and I'll put money down that it's not a "forever" bike for you), at least not until it NEEDS paint from use and abuse.
Skip the ammo cans, they are WAY heavy and very small for what they offer. You'd be better off with cheap soft saddlebags and a milk crate or "tough tote" on the top for hauling duty. Hard bags on the side also have another issue, they tend to be leg breakers if you "dab" while off balance and dont manage to get your leg out of the way in time. We saw several guys a year experience this back in CO (usually on BMWs). I ran the "Original Side Rack" with Ortleib soft bags when touring. In any case, I'd spend more money on making the bike ride and fit right first.. bar risers (as needed, I needed +2inch at 6'4") were essential for me. Same with stiffer front springs and a replacement rear shock, a braided front brake line and full service (the swingarm and linkage on mine were nearly frozen solid, and the bike was a "babied", 5 year old and 8k mile example). I'm on the fence with the "doo", it's cheap and easy but I think it's mostly internet paranoia that drives this cottage industry.
Don't skimp on the protective gear, too many txting teens out there on the roads that think it's okay to bump into other traffic at speed. You have no control over someone else tagging you.... and I hear that crashing without gear sucks, though I've not experienced it (crashing WITH gear is bad enough).
If you absolutely insist on going "military", try finding some Mermite cans (aluminum, used to transport hot/cold foodstuffs) and try to emulate the M1030M1 (KLR with diesel plant from HDT that's actually used by the military):
http://upload.wikimedia.org/wikipedia/commons/5/54/M1030m1.jpg
No idea where you're located, but if you need any mechanical assistance, I'm a pro MC mechanic at the south end of Meriwether county and will gladly help out. Give ya a discounted rate on any work you just want done, otherwise just a donation (pizza/beer type) for helping out would be appreciated, but not required. :)