Brian,
I ran mine for half a summer with nothing done but the AI pulled and the pipes added, so yes you can do it. With the AI pulled I had quite a bit of popping before I tuned it, but I'd imagine the popping would be much worse without it. You can TOTALLY do the AI yourself, it's super easy! If for no other reason, you should pull the AI before your header pipes turn blue.
The first video I took (which is posted on my site) was taken before I modded the cannons while running 45 pilots, one shim, and stock main jets. Why that combo? Long story short... I pulled my carbs and rejetted the pilots. Next I went to do the main jets and noticed the new ones were the wrong size, they were actually *smaller*. I threw in the shim and waited for the new main jet. In the mean time I took the video. There is noticeable popping every time the bike slows down in the video. That was actually better than before I rejetted the pilots and added the shim.
So yes, you can run stock jets with pipes, but it's such a waste considering how much untapped power can be had for spending less than $10 on jets and pulling out your snorkel in the airbox. It's huge.