Trevor - knocking on hot start up (putting all the info we have heard so far together) is the sound of the tensioner. It does it when hot, as the viscosity of the oil when hot, allows the tensioner oil to drain.
It's a peculiarity of this bike and I would suggest, it's of no concern - just like the cam shaft knock on your 40 year old Suzis.
As for the vibration, I agree it's very annoying. I can only assume that the new camshafts have been installed without recourse to altering other internal engine components, to match the new rotating mass.
I have 90% over come this issue with slight fuel map mods, adding extra fuel over the vibration zone (4,600 - 5,600 rpm) on the IAS and TPS maps (as per dark blue areas on the pics). Also turning off the O2 sensor (which is constantly trying the lean out the bike).
At some stage, I might even try backing off the ignition advance in these areas, to help reduce the ragged feel.
It's a 10 minute job to do this with the Woolich Racing tuning software. Find someone with the kit. You will have to pay about $100 to Woolich to install the tune on your bike.
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I can't help you with the seat issue, other than to try using some cycling shorts that have extra padding. My solution is to follow my Dad's example, when he toured to US on a 1983 Suzuki GS1100G - a nice soft sheepskin.
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