Sounds like you have your bike up and running. That's good!
The extra room in the basket created by removing the friction disk means a longer lever throw and it should translate into making it easier to find neutral. Also, since the clutch spring pressure is reduced, you might want to test your clutch for slippage (once you have the cable adjusted properly). If there is slippage it could mean you have a long clutch basket and did not need to discard the one friction disk.
Since you went straight to step #3 you don't know for sure if the pressure plate is correctly oriented, nor if it was necessary to remove the extra friction disk. But, hey, if it works to your satisfaction, why make trouble?
I wanted to save this for the last...because its rare in street use and unpleasant to deal with....but there is one more concern that your situation exposes. One symptom is a clutch lever that feels rough when squeezing and does not pull smoothly towards the handlebar and a clutch that often drags or bounces before releasing.
Here's the explanation: Since you had an oil shortage problem inside the clutch, you must be sure that the inner and outer baskets are not worn excessively. I can't really tell from your pictures whether or not the inner hub is worn. I see the glossiness created by the plates, but if you ran your finger down the groove: Are the glossy areas indented? If they are well worn, then the plates have worn a pit for themselves and will resist moving smoothly along the hub when the lifter is actuated. The friction disks can make similar grooves in the clutch outer drum with the same effect. Lack of oil precipitates this condition as does "snap" releasing of the clutch lever. Unfortunately, the only remedy in that case is new parts.
Like I said, its rare and usually found when the clutch outer has been stretched causing excessive play which further quickens the creation of these grooves. Never-the-less, it might be worth checking.