My thinking is that there's nothing wrong with the recipe-just that the process is different. I've got several of Stone's recipes in their book, plus from a few other locations. All of their recipes seem to have about 35% fewer IBUs than their advertised levels. Because of the consistent ~35% difference, I'm thinking the difference is process related. (Note-there are some outliers in the data. That Stone Pale Ale recipe is one, far more than 35% for that one.)
Also keep in mind I'm using the blog/book recipe, which was slightly different from the recipe that you posted.
It's not just beersmith, even doing these equations by hand will show the expected IBU levels to be far below the Stone-advertised levels. I'm just using beersmith to "gauge" how slight process changes can increase the IBU levels.
As for what I'm aiming for, I'd say I'm trying to get as close to Levitation as I can from all the data that I have. I've never had this beer fresh, typically most Stone beers are pretty close to their drink by date when they make it over to this side of the country. Hopefully Stone's new Richmond brewery will help solve this problem, but by then Levitation will be gone.
So all I have to compare it to is the posted data and thoughts from when I've had the beer well past its prime. Hence why I'm trying to reconcile the recipe with the advertised IBU levels. I remember this beer being distinctly bitter, but not a lot of hop aroma since it was old. I don't see the 22ish IBUs the recipe shows being nearly enough to get that effect.
That's the goal from this batch. If I brew this again I may change things up based on my preferences. Get rid of some of the crystal malt, maybe swap some hops around, etc.