I've done this before on a DRZ (KTM wheels to DRZ).
You've got a couple of things to address. First of all, axle sizes. Are they the same? Are they different?
Second of all, you need to establish the appropriate offset for the wheel, to make sure it's in line with the rear.
Third of all, you need to properly line up the rotor.
If the F3 wheels have accept a larger axle than the KLR front axle, you'll want to get some sleeve spacers. Other option is to try and find bearings with a smaller ID, any bearing house (or the internet) should be able to tell you if that's a possibility or not. Then it's a matter of measuring things out and going from there. The other option is a custom axle with the appropriate sizes, although that has it's own pitfalls.
Depending on the front rotor design, you might be able to space it out, you might have to compromise slightly in some way or another.
Honestly, if I were doing this, I'd find a set of KLR hubs and get a set of 17 inch rims laced to them. They'll handle abuse (curbs, jumps, etc) much better, and you won't have to worry about offset, rotor fit, etc. If you want to upgrade the brakes, you can pick up an EBC 320mm kit that comes with the appropriate adapter to space out the stock caliper to accept the 320mm disk. Cheaper, easier, keeps stock parts, more salable in the future, just a better solution for a dozen and one reasons.
When I did it, the KTM rear was a straight bolt on, the front just required a custom axle and spacers, which made it moderately ok, although there were some things I really didn't like about that setup either. And I had a devil of a time getting the axle made right, I ended up having to go to a machine shop and cut it down and rethread it myself. Sigh.
Feel free to ask any questions.