There are no 03 R6S models, only R6 - that's first, so if you see an S on the fairings, it's an 06 - 08.
Get the vin for the bike and call yamaha with it, ask if the coils were changed when the recall was made for the 03 models. If you want to check your self, just pull the coils (will take about an hour if you know what your doing) and check that they are mitsubishi coils, not Denso.
If they weren't changed, it'll be around $60-90 per coil.
Ask about coolant change - when was the last time? open the reservior and have a look inside for debris and stuff, (this is just to let you know how well the bike was maintained and how honest your seller will be) - debris often means old coolant.
Before you arrive, ask your seller not to start the bike, leave it cold. When you arrive, turn the key, watch the lights on the instrument panel. Flip the engine cut off switch to on, listen for the fuel pump whirling. Press the starter, how long does it take to come on?? Listen to the engine, ignore ticking, you're listening for knocking, heavy sounds, stressed sounds (helps to cover the exhaust for a moment after the bike is warmed up, you can then hear the engine, but do this only for a few seconds).
Ask about the engine oil and filter - what what his/her change cycle (should be every 3000 miles, and filter every other time at least, if not every oil change). Then ask when was the last change and with what weight. If you know what different grades feel like, then check the oil for color (should be brown, not black) and viscosity, ie. yamaha would use 5w-30, 10w-30 or 10w-40 in this engine, so when you pull the dipstick, the oil should not run too fast, should want to stick to the to the dipstick a little.
Check the chain, tension should be right if the bike is being ridden, and shouldn't be rusted or you'll need to change it/clean it really well. Put the bike on a stand if possible, and roll the back wheel to check for loose/overly-tight spots on the chain. Too many means changing time and $$$$.
Check the tires, if the bike is stored for long periods on the side stand, tires get flat spots, which again means $$$
while the bike is idling (after it's fully warmed up), open the throttle a little then let off, make sure it returns to idle speed, not below idle speed. Otherwise, $$$
Those are what I can think of at the moment off the top of my head. Good luck!!
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