You'll have to help me out here... I have been on Gixxers forever and just bought the 03' 636 so I'm not sure if the previous model years have been F.I.???
If so, your ticking is probably the fuel injectors cycling. I have been an ASE Cert. tech at a GM dealership for a long time and I hear the same question from many many people regarding their cars.
If your bikes are not F.I., the most likely causes for a ticking sound are 1.)hydrolic lifters, 2.)excessive valve lash, 3.)worn cam lobes, and 4.)weak valve springs. Now, #1 and #3 are out due to the engine configuration, #4 is usually not an issue with high rpm capable engines and #2 should be checked and adjusted periodically anyway.
From a mechanics standpoint, ticking is not usually indicitave of something altogether bad... knocking, such as main bearings, connecting rods/pins etc. almost always mean bad things.
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