Update:
After a couple of drain and fills, I did a filter change, dropped the pan and filled the sump precisely with 3.5 ltre.
I noticed when I dumped the oil, there was a lot of oil. I didn't measure but it was a lot. So I filled it by measurement, rode the bike, let it sit and checked for leaks after a couple of hours.
I checked the oil level on the side stand. The dipstick showed the fill at the full mark (but not the painted mark from PO). I can only conclude that level is meant to be checked when the bike is on the side stand- not being held upright level. The bike isn't puking oil either.
I can conclude that I was over filling the crankcase by trying to compensate for checking the dipstick while on the side stand. The full mark is indeed full when the bike is on the side stand.
I did clean quite of bit of oily grime under the tranny and swingarm. Also changed the tranny and rear end (+moly). Valve adjustment and plugs tomorrow.