Hi Travis -
I think your suggestion for some good new oil is a good one, you don't know how long that oil has been in the bike already (likely since new). All of my bikes shifted better after an oil change, and the ninjette is no different. What I'd also try is to adjust the clutch cable to make sure that when you are pulling the clutch lever the clutch is completely disengaging as it should.
Here's a link on how to adjust the clutch lever (it's a snap).
After you've done those two things, I'd concentrate on making sure that each shift you make is firm and positive, and see if the symptoms go away. You can also adjust the shift lever itself to put it in a comfortable place for your boot, so it's positioned just right for good shifts up and down. The ninjette transmissions are reasonably bulletproof, there is little talk of early failure on them and at 400 miles or so, there's no reason to believe yours is already broken in some way.