Hi ekoja!
By saying
ekoja wrote:... It also will not engage the starter whilst it is in gear but with the clutch in and the sidestand up. ...
... I understand that the failure to start ingear with the clutch in will possibly be a cutout switch thingy but I wonder if there is a connection between the two ...
you mean with the clutch engaged (i.e. the lever not pulled)? Sorry for asking, but I'm not sure and I'm only trying to help ...
If so, that's normal that the starter will not work because of a little switch in the clutch lever by which it is determined whether or not the lever is pulled. In combination whith not being in neutral, the starter is blocked. (Although I suppose you already know that ...)
As to the clonking first gear:
As some had written before, there are some methods for avoiding it:
Before starting:
- selecting a gear (I prefer fourth) and pushing the bike with disengaged clutch for releasing the clutch disks which stick together yet (also because of the cold oil); then shifting into first and start (with pulled clutch lever of course and functioning clutch lever switch

)
If started in neutral:
- pulling and releasing the lever several times (approx. 5x) before shifting (for preventing the clutch disks from sticking together)
- holding the lever pulled for about 5 seconds before shifting (for letting the gear shafts come to a standstill)
Even with warm engine, I do holding the lever pulled for about 5 seconds before shifting when starting from a traffic light because of avoiding the "clonk".

A low oil level can also intensify the "clonk" effekt.
Hope I could help a little.
ekoja wrote:Now about my difficulty in engaging first gear.

Errm, any further details
