Clutch travel is relatively small, don't think 12 inches sounds too small, too much if anything?
The biting point is quite low and can be snatchy if you're not used to it.
No idea as to engine warning light as result of fuel cap, I think they all had Yamaha fuel caps from memory? Pretty sure my S2 did. However yellow engine warning light on is not uncommon.
Not sure any of it helps but good luck!
