Most are 5k in fact, it's unusual to find a 10k specified.
While youre ordering stuff check the correct plug is fitted too, I assume a non resistor type plug should be fitted...check the manual, FYI resistor type plugs have an 'R' in the code
here's a 10k cap
http://cgi.ebay.co.uk/NGK-Spark-Plug-Caps-LB10EHF-Red-5mm-HT-Cable-/220810886862?pt=UK_CarsParts_Vehicles_CarParts_SM&hash=item33695abece
so do i assume the coil secondary measures what you said minus this 4900 ohms? or did you measure it correct with the cap off?
Now you have found a difference between your bike and the manual can you be sure the manual is the correct one for your year/model bike?