I loved Japanese Onsen and always felt comfortable. Off course people look at you, but i didnt have anybody stare at me (unlike in Korea).
I have only been at one mixed Onsen wich was ok (mostly man).
I have been at over 30 different Onsen and i never felt that i got special treatment because i am a gaijin... My best experience was an Onsen somewhere in Kansai wich was open to the Seaside. Not to far away was a bridge from wich you could see inside the male-side. Sometimes people would walk by and stop for a moment and look, suddenly this guy next to me (maybe 25) gets up and waves at the people on the bridge
they just ignored him... "we didnt look..."
To the car thingy: I have been driving in Australia and Japan (im from germany) and i got used to driving the other way round very fast. Because you are also sitting on the other side it usually is no problem. I think driving a scooter might be more difficult to start with. Id also recommend to rent a small car first (K-Jidosha), just got to you local Toyota rental-car, they have the best prices.