Between three and two years ago I went through the same process you are beginning - equipping a KLR 650 for a rtw trip, although my trip was not nearly as extensive as the one you are planning. I currently have about 27K miles on my 2004 KLR and it's been totally reliable. Although some disagree, I believe these bikes are excellent choices for extended adventure riding. I did many of the modifications you list in your post but not all. A complete list of what i did to my bike is on my website, www.rtwrider. net. FWIW, some comments relating to your list of proposed modifications/upgrades follows, and some suggestions for things you didn't list. Btw, I'm assuming you will be riding a pre-2008 model KLR - I have no experience with the 2008 model.

Your Vital Changes:
Radiator Fan Blade (metal): Somewhere I read of problems relating to the metal fan, something to do with the fan coming loose and the metal blades piercing the radiator, if I recall correctly (which I may not). I left the stock fan on and had no problems with it, even though I have crashed the bike and bent the fan housing (the plastic blades did not break).
Acerbis Rally Pro hand guards: I would put hand guards in the vital category, but Acerbis would not be my choice. I prefer the Factory 909 Masher (or similar) guards which have an articulaled mounting system and are easier to install and equally protective.
Sealed Bearings: I didn't do this and had no problems that would have been avoided by sealed bearings, but have no experience with the sealed bearings. They may well be an excellent idea for a journey as long as the one you plan.
Progressive Springs (rear): I'm not sure if you mean just a shock spring or the entire shock - spring combination. I strongly recommend replacing the entire stock shock. My Progressive shock has about 19000 miles on it and still functions extremely well.
I did everything else you list in this category and agree they are all excellent improvements.

Convenience Upgrades:
I did all of these except the speed bleeders and LED turn signals. I'm sure there is nothing wrong with doing both of these but I didn't think it was necessary.

Rejected:
I did use a centerstand and do recommend it unless ground clearance will frequently be vital to you. The convenience it provides for fixing flats, changing tires, lubeing the chain, etc. was very valuable, IMO. The weight is carried very low and I did not notice any effect from it. Ground clearance is reduced somewhat, however.

Unknown:
Drive Chain: Mine had a master link. I would suggest putting on the best, strongest chain you can get but I'm influenced because this was the only mechanical problem I had, unless two flats and crash related problems are counted. I strongly recommend against Krause Sidewinder chains - that's what I used and it broke three times.
HID Headlight: I have no experience with these. I simply installed a higher wattage H4 bulb and took a spare. Probably an excellent idea, if for no other reason than because of less electrical current draw.
Heated Grips: Depends on the climates you will be traveling in. These don't need to cost a lot (Dualstar sells a set for not much over $25 that work surprisingly well - I don't have them on my KLR but on another bike). If in doubt, get them since you don't need to turn them on unless you want to, and they can make a huge difference if it's really cold (there was a time or two in Siberia I wished I'd had them, even in August!!).
IMS Tank: I really like mine (which holds more than the advertised capacity - a measured 7.5 gallons). The protection for the fan, radiator, and coolant tank are better than any other method, and the plastic used in these tanks is really tough, tougher than the steel stock tank I believe.
Nerf Bars: Good if you don't get the IMS tank, but the tank is more protective. These aren't as heavy as they look; they're hollow and actually quite light (I had a set on my KLR until I bought the IMS tank).
Radiator/Reservoir and Water Pump Guards: I didn't get them and never regretted not having them.
Fork Brace: I like mine (Happy Trails), feeling it gives a bit more stability both on and off pavement. OTOH, a friend felt his caused binding of the fork and took it off his KLR. Not essential.
Locking Axle and alignment nuts: I have both and they do make work on these areas easier. Mine have held up so far (again, about 19K miles). I especially prefer the locking alignment nut over the stock double nut system.

Other suggestions/recommendations/comments:
Rather than just a stainless steel front brake line I would recommend an entire front brake upgrade kit, including the larger rotor. The stock front brake on the pre-2008 KLRs is so woefully inadequate for pavement riding that I don't feel just a stainless line is adequate, at least for my riding. Dual Star brought out a kit for about $200 awhile back, a considerably better price than what was previously available.
Headlight protection of some sort. I have a robust metal protector made by Big Cee engineering. However Big Cee is apparently no longer in business (although he has a great FAQ section about the KLR on his website, www.bigcee.com. I highly recommend you read that if you haven't already). Arrowhead Motorsports still markets a metal guard, last I knew. Even the stick on vinyl covering (by Dual Star I think) would add some protection.
Happy Trails engine guard - highway peg combination. I really like this unit. I'm not sure how much protection it actually provides the lower motor area, but for my money just the highway pegs are worth the cost. When one is riding substantial distances day after day after day, having a second foot position is invaluable, IMHO.
Bypass the side stand lockout. Sooner or later the contacts on this become corroded and then the engine dies when the rider starts the bike moving since it "thinks" the side stand is still down.. At one time Totally Wired Cycles sold a plug and play kit that bypassed the side stand and clutch lockouts, and this was switched so the rider could choose the bypass (either or both) if they desired, such as when a problem started. But, I don't see this on the TWC website any longer. Tammy (the owner) may have discontinued selling this because of liability issues. Alternatively, it's simple to bypass the side stand lockout by altering the wiring.
Supposedly the fan relay has been known to fail on KLRs, rendering the fan inoperative, although I've never heard of this actually happening to anyone's bike. Totally Wired Cycles sells a bypass kit for the fan relay so the fan can be operated via a switch if the fan fails. I do have this on my bike and occasionally have turned on the fan and operated it continuously when riding off-pavement in difficult conditions at very slow speeds in hot weather. This avoids the repeated on and off cycling of the fan that occurs in this situation.
I have rim locks on my bike, but am not sure how important they really are for a KLR. They do make tire or tube changing more difficult and the tires more difficult to balance, although it still can be done. I do recommend ultra heavy duty tubes for this type of travelilng. Not everything advertised as a heavy duty tube is the maximum 4 mm thickness. Bridgestone and Fly Racing are two companies that do sell real 4 mm tubes.
Skidplate. Yes, I think they are worth the extra weight, which is carried very low on the bike and not noticeable. With a skidplate and low profile oil drain plug the plug is totally protected. There have been times when I've "banged, for lack of a better word," over large imbedded rocks, or in one case a tree trunk, and been very grateful I had a skidplate.
A billet aluminum mount for the left side mirror. The stock arrangement is for the mirror to mount directly to the switch housing on the left side and in a crash this plastic unit may be easily broken.
A stronger, lighter handlebar. I like the Protaper SE Atv High bar. It also vibrates less.
I've never met anyone who likes the stock seat. I have a Mr. Ed's Moto aftermarket seat and like it.
Dual Star sells a stronger, billet aluminum, mounting bracket for the rear brake lever. I have it, but am not sure how important it is (there are probably much more important things to spend money on).
I have a lockable storage compartment that fits underneath the license plate and used it to hold spare copies of my important documents. The idea here is that the unit is somewhat hidden and would be missed by thieves. I don't recall who sells it - probably Rider Warehouse or Whitehorse Press.
Speaking of security, for a trip like this I would recommend metal or hard plastic panniers and rear top box. I was able to fit everything I took in these three boxes so nothing was exposed and enticing to thieves. This is also preferred for weather protection. However, rigid panniers do create an increased risk of a lower leg fracture if there is a crash and a leg gets caught between the pannier and ground, so keep those legs forward!
I also installed a Nady remotely triggered motion alarm on my bike which also signals the remote switch that the user carries with him/her and strongly recommend one of these. It was interesting that in Russia most vehicles have these.
Tim at Happy Trails recommends aftermarket fork gaiters that drain better than stock. I have them, am not sure how valuable they really are.
Scott Oiler - I'm ambivalent about this. I don't think this is the best way to lube a chain when riding in dirt, and I was never able to get mine set so that the chain seemed adequately lubed without throwing lots of oil. As mentioned earlier, I had chain breakage problems but I don't believe this related to the Scott Oiler. It also quit working about the time I finished crossing Russia because a small hole devieloped in a tube; I had never used one of these before my rtw trip and took it off when I got home, never using it since. If you want mine you may have it for the cost of shipping (it has the larger expedition reservoir).

Anything on your list I haven't specifically mentioned I do have on my bike and am happy with it. Doing all of this may seem a huge expenditure of time and money, but KLR's are so inexpensive to purchase they are still reasonably priced even after all the modifications. And some of us, myself included, greatly enjoy doing improvements and making a bike better for it's intended use. I certainly enjoyed working on mine.

That's all I can think of at the moment. If you have any questions send me an email (the address is on my website). I hope all of this is of some help. Good luck and enjoy what should be the ride of a lifetime.

Mike
Idaho
www.rtwrider.net

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Mike