I don't know exactly what of this will translate to the LC4's, but most of it applies to the RFS 4T's and all of it to the 2T's...
Skidplate: The Devol skidplate is far and away the one of choice for the 2T's. Rather than micky-mouse hooks, it uses a piece of flatbar across the framerails with holes drilled (sort of visible below). Seems to stay in place very well, provides good protection, and not too pricey.
Stay away from both the KTM hardparts plate, and the enduro engineering plate. Both are undersized and made from thin material.
Enduro Engineering sells a kit to relocate the CDI out of harms way, under the tank. In it's original position on the frame near the steering head, it is vulnerable to crash damage in odd scenarios, and if the steering stop bolt ever vibrates out, the forks will hit it and ruin it. And putting it under the tank allows you to dial in some more steering lock. Money well spent.
The front brake line will cut into the clutch line, if given the chance.
My solution is low tech- I just put some fuel line around the clutch line and keep an eye on it.
I also wrap the brake line/odo wires in some of that expandable plastic sheath (visible in the photo above) to protect against chafing. Seems to work.
The shock location on the 2003/2004 bikes flat out sucks:
My boot rubs heavily enough to wear through the shock body in about 1500 miles. GRRRRR! Had to buy a new shock:
On the plus side, I got one off Mike Lafferty's bike right when he broke himself, and it's magic. Whatever special sauce they use seems to have made it into this thing... solution is to buy the e-line carbon guard for $40. No issues since installing one.
Speaking of e-line, their carbon pipe guards are the best solution I've found. I've tried both Pro Circuit and FMF Gnarly pipes, and prefer stock for the way it makes power... and the e-line guard has protected it in some horrific hits.
Now for a big one. All KTM's I've seen have a thermostat housing right behind the radiators like this:
On this bike, it hasn't done much, but in many cases the corner will rub into the radiator over time and cause leakage. My solution is to safety wire it back to the tank mounting point, so that it just can't QUITE touch. This is worth a look, on both 2 and 4 strokes!
Speaking of, that plastic "Y" fitting on top of the motor is a weak link. Whenever you do a top end, inspect it for cracks or other signs of wear. If it breaks, you'll have no coolant in a hurry and it's a good way to ruin your motor and your day.
The kickstand is another weak point, in that it is not designed to bear any load more than the bike, and it's easy to break the mounting bolt.
My suggestions: loctite the bolt, and keep an eye that it stays tight. If it loosens, you'll break it off very easily. Put tri-flow (bicycle teflon lube) on the kickstand to keep the action free- one application will last quite a while. Finally, use the little rubber strap provided to hold the kickstand up when not in use- my experience has been that the bolt will not tend to loosen if the kickstand is supported by the strap.
Unlike Jap bikes, my KTM swingarm pivots have always been reasonably well greased from the factory. The Heim Joint and the upper shock mount needle bearing will eventually wear out, but the original KTM parts seem to last well and are not unreasonably priced IMHO. On very high mileage bikes, the mudflap hanging down in front of the rear wheel will begin to eat into the swingarm aluminum- several companies make guards to help prevent this.
The Enduro Engineering Sharkfin (brake disk guard) is cheap and effective. Good insurance for the rear disk. The bolts like to vibrate out, so loctite them (or weld the bastard on if you want to be sure...).
Can't think what else for the chassis... Dirtrider will no doubt be correcting me here shortly...