Looks nice Drew - good for you. One thing: I would not rush to ditch the air box right away. It works well and stock filters are still available - plus the stock carb jets should work well with it. Same with the stock exhaust.
The first rule of troubleshooting a machine is to change just one thing at a time, test and observe. I'd get it running in stock condition before starting to mess with it too much.
Have fun and play safely!
Pete