First of all, I admire your gumption in planning and embarking on such a trip! It sounds like it will be a blast.
I don't have all the answers, but will say a couple of things in regards to some of your questions.
Balancing tires isn't that critical on a KLR. I've never balanced any of mine. The most rudimentary method would be to just put the wheel/tire back on and spin it and see if one side tends to spin down to the bottom, which is unlikely.
No idea about the chain: how many miles are on it? 4800? Shops recommend a lot of things. Sometimes they're legit, sometimes they're just trying to make some money. I would think even a neglected stock o-ring chain would be fine at 4800 miles.
Changing tires is not that hard, but can be frustrating when you first start out. Just Google "motocross tire changing" and you'll find some good videos that will explain the process better than words ever can. I suggest "motocross tire changing" because those tires have tubes in them.
There aren't really any kits available. You have to put together your own tools. Here's a thread that discussed tool needs for tire changes:
I use the Eagle Mike Quick Jack and like it.
If you think you might encounter large rocks, I would definitely drop coin on a metal skidplate. A busted oil drain plug/cracked threads/case could have you heading to Hertz to rent a car to get back home. There have been some real horror stories on here from riders who were unfortunate enough to have some object strike their oil drain plug and bust it. The stock plastic skid plate provides very little protection for the plug.
I have the HT guards, but stand strong in my opinion that they are probably the worst choice for the KLR as opposed to other offerings like Givi or SW Motech. Some people have no problem with them, but it's been my experience that the inner support bars are too fragile, bend/shift easily and pass too close to critical components like the voltage regular and radiator.
I would think at 4800 miles your doohickey would be fine for the trip, but I would make sure it's adjusted.
When are you going? I'm not a long-range rider, but the old mantra of "don't do any serious maintenance or mods you don't have to do right before you leave" makes a lot of sense to me.
I wish you luck on your trip! We will expect photos........