... I wish I had access to a KLR similar to mine with the suspension upgrades you keep mentioning to see what the difference really was in terms of my comfort, control, and abilities on the bike. I really dig my KLR, but most of the off road riding I try to do is pretty challenging. I'm going out in the desert where I used to take my WR250F and I struggle a lot with the KLR. I am running TKC80's and feel reasonably good about those. I picked up a low profile Sargent seat which has helped tremendously. But, I still have a very hard time and not a particularly fun time taking the KLR in to deep soft sand or challenging single track climbs.
I've considered going to the D606's the next time I need tires, but that's a ways out. My theory on the low profile seat is that it both gets my feet closer to the ground when needed (I'm only 5'10" with a 30" inseam) and puts my weight a little lower in the bike when seated (I tend to spend a fair amount of my time offroad on my ass unlike most people). I haven't noticed my shocks really bottoming out or trying to throw me, but the front does feel sort of soft to me and I don't like that I don't have the same adjustments available to me as a dirt bike. So, I feel like I have a great road bike that likes gravel and dirt roads, but isn't fun on trails.
I'm an experienced street rider with a variety of types of bikes, but only picked up dirt bikes and off road riding a year or two ago. So, I've always just chalked up my struggles on the KLR to my not being a particularly skilled off road rider. Of course, I question that again anytime I get on a true dirt bike and your posts about suspension on the KLR's keep making me wish I could try your suggestions before paying for and performing those upgrades. I've already sunk a lot of money in to my KLR, most of which has been worth it, and it's tough to consider major significant suspension upgrades without knowing what the result will be.
Your logic on doing as little as possible to the stock suspension or going all-in with big suspension upgrades makes a ton of sense to me though...