I don't know this to be true, but i think the long bolts that were included are actually for another application. If you go to the AC Racing site and look at the nerfs for the Z400, they are almost exactly alike. With one difference. Those long bolts i believe are the new front motor mount bolts that get used on the Z400 install. I think AC just used the parts pack from the Z400 application for the Polaris application to save some money. Thats my guess. I did not use them. I suppose that you could drill the pegs and use them for that but i did not find it necessary. There is a little play on each side on the pegs but i can live with it.
I did not buy the aluminum airbox. I just did not think it a necessary buy for me. I still think its a good thing, just not for my riding. I just modified the stock airbox and rejetted. I use the clamp on filter without the airbox in the dunes and change the jetting. It works great in a non-wet environment.
I think you should consider a pipe before you do anything that would increase the air/fuel flow to the engine. Your engine needs to "exhale", so to speak, and the stock exhaust just will not cut it in my book. You could make the changes and keep the stock pipe and be ok, but you will not see the full potentail of the modifications if you don't put a pipe on it. That's just my opinion.
My jetting is as follows:
WIth a pipe and airbox modifications(includes drop in K&N filter), i run a 160 main, 45 pilot and air screw out 2 1/4 turns.
WIth Pipe, clamp on K&N filter, i run a 170 main, 50 pilot and airscrew out 2 1/2 turns.
Now, these settings work great for me. it could be different for you. I ride anywhere from sea level to 3000 ft above sea level. it seems to work good for me. On the track, with the K&N clamp on filter setup. no one can touch this bike, not even the new YFZ's. The predator handles way better than the YFZ and that lets the power show through. to bad i am getting rid of my predator.
Good luck with your stuff. i hope i was of some help. glad you like the propeg nerfs. i love mine.