Good evening!
I am not sure if this will be read but due to the current state of health and such, I am trying my hardest to resolve my own issues before going to a mechanic. With that being said, here goes nothing:
I'm a new rider and purchased my first bike to learn slowly and properly (2006 Ninja EX250). I spent the whole week riding and was really enjoying myself, wast practicing riding with some friends and ended up dropping the bike at about 10 mph, causing the stator to crack open. That same day I went home, did some googling and purchased the parts, replaced the stator and am now having shifter issues. The bike will go in gear and back to neutral but will not go past 2nd gear. Feels as though it's blocked off whenever I try and shift up. I went to a local bike shop and he recommended adjusting my shifter, took some tries at it and nothing. Will ultimately end up bringing it to a shop if I can't find a fix, but here are some photos. When I opened the shifter case and took a look I did not see the spring shown in diagrams, not sure if that's inside the actual transmission side.

The rod does not seem bent
I removed most of the gunk on the rod itself (after I took the picture)
I have tried re-aligning the shifter but it doesn't seem to work, I'll give it another shot
The shifter shifts well from N -> 2nd

Any tips or advice would be greatly appreciated. Thank you!
Please see images below.

 

More than likely, it bent a shifting fork. My bike (an 04) doesn't have that spring you pointed out on the outside of the tranny case either. Good luck, let us know what you find.