Since purchased second-hand in 2003 from an individual, I have had issues with the carburetor. When I went to look at it, the bike would not start and run because of fuel flooding. I bought it anyway and tore down the carb, but found no obvious faults, so I can only assume it was trash in the float.
Just last year I found trash in the slow air jet inlet when it started a repeat performance of the flooding I experienced in 2003. My opinion is that the stock air filter is, even when cleaned and oiled regularly, a poor performer because it allows un-filtered air to bypass at the base. I HIGHLY recommend an after-market air filter as well as one or another air-box modifications, which allow more airflow.
Additional fuel filters are not recommended unless they are designed for gravity-fed small engines. Automotive fuel filters are designed to filter under pressure from the fuel pump. There are however some after-market right-angle filters that have received favorable remarks.
The KLR is NOT for those with short inseams (mine is 32"). Nor is it for beginners. It is an old design, with very few technological updates, but it is torquey and top-heavy.
It will pull a wheelie in first gear, and it will take itself and a 200 pound man 3-4' in the air if you care to jump it. It will drag the pegs in a turn, and not lose traction if you're not afraid to lean.
I love it and I'd recommend it for all sorts of riders (except as mentioned above) with a few warnings. The seat SUCKS! It's adequate when new, but as it ages the foam is useless. I've tried sitting on a Corbin flat seat and it seemed hard. Corbin does recommend allowing hundreds of miles of run-in before you will find it comfortable. I'm not sure it's worth the outlay yet.
If you're not used to a dirt bike (and top-heavy at that) you're gonna drop it, and the first thing that's gonna suffer is the radiator. Get a radiator guard FIRST. Then, get an IMS rally tank in your favorite color, and you won't have to worry about the lower tank covers anymore. Also if it spills, your swing arm is gonna get gouged by either the passenger peg bracket, or the kickstand. Just thought I'd warn you. There is a lot a great information and links at Big Cee's KLR FAQ page http://www.bigcee.com/klr650faq.html
I have yet to have an issue with the cam chain tensioner (doohickey), and while I did change the brake lines to braided stainless steel, I've not seen a tremendous improvement, nor do I expect you could brake any harder without skidding.
The best advice I can offer is "Be Alert". You have to brake early and downshift appropriately to stop without taking off valuable rubber from those high dollar dual-sport tires.
Which leads me to the oft' asked question 'which tires...?'. Mine came with AVON Gripsters, which were great for the street, but absolutely useless anywhere else. The most recent purchase was a set of MAXXIS C6006 DOT knobbies and Heavy Duty inner-tubes that I am very happy with. Except for the initial break-in (both tire and rider), they bite better on the street, dirt and mud, but they are noisy. So I wear ear plugs.
Also, because I like to ride in cooler weather, I went up to an NGK DP7EA-9 plug. It keeps the engine temperature up in cool weather, and I haven't noticed any over-heating in hot weather yet.
All in all, it's a great bike. I ride it hard, but I try to give it all the attention it needs so it won't leave me stranded. I have called it every name you can think of (and some you can't) when it let's me down on a trail. But it always takes me home.