Is this bottom end put together correctly?

Hey guys. Made a video. I just want to make sure everything is installed correctly before i put the crankcase together. Its a 07 honda 400ex. Does it matter what gear its in when put together? I feel four points when shifting. I assume its correct cause neutral + the 4 .You can see it and hear it in the video.
Also, may sound stupid, but the bushings in the diagram that go in between the gears on the 2 shafts have a hole. I assume this is to allow lubrication of the shafts. Do they have to be lined up with the holes in the countershaft and mainshaft? Or does it not matter, cause they will spin around? I just want to make sure. Please let me know if you see anything that needs attention. everything seems ok to me. thanks

http://www.partzilla.com/parts/searc...ION/parts.html

https://www.youtube.com/watch?v=IGNmRH8DPlI