Wow, those seem like big jets for your elevation! I don't have a clue about it though cause I've never ridden Doo. Your right, gutting the airbox should give you more air...and more revs. Obviously more air means leaner condition so check your plugs and have a set of bigger jets ready to install...one size should be enough. If the revs don't go up, I don't think you gained anything and should probably put the airbox back to original.
I jetted my ATACC for 1700' and -20. With the gutted airbox, I put 440's in, raised the needles one clip, and installed 1 size bigger pilots. I had a slight burble when coming off idle that disappeared almost instantly...more of an irratation than anything...adjusted fuel/air screws and got rid of it. I checked plugs at various elevations and throttle settings...all was good. The highest I've ridden is about 9000', most of the time we are at about 7000'. Best test was on a lake at 2700'. Sled was warmed up good and I pinned it for 25-30 seconds and plugs were perfect. Synthetic oil makes piston wash almost impossible to read. Cat's factory settings for midrange was too lean, and caused lean seizures in numerous sleds, including one of my buddies. He got it fixed and installed ATACC and jetted exactly same as me. I was lucky enough to install ATACC when sled was brand new, and rejetted everything before first ride. We removed heads at end of last season and everything still looks like new. The lean seizures were less of a problem for guys that ride with dirt bike mentality...constantly varying throttle position. Sounds like lean seizures were typically a result of prolonged trail riding at constant mid throttle position, which is exactly when my buddies went squeak. I have a tendancy to point and squirt!
Now, with The Thing installed, I rejetted to 390's based on experience of others with same machine and similar mods. I asked manufacturer of the Thing about my midrange jetting possibly being too rich now, but he said it shouldn't be a problem. This is possibly due to The Thing building the higher vaccum at 3/4 throttle and higher, when your engines on the main jets. I don't think The Thing changes much at low and medium throttle, but I could be wrong. I'm still learning about this Thing and will obviously learn alot more after a couple rides.
As for your lower end, it may also just be a matter of adjusting the screws slightly. I guess you'll know when you ride it. Be careful if it's running crisp...I know it feels good, but crisp usually indicates running on the leaner side of safe. Remember, they run the best right before they go squeak! Do some plug testing at low and mid throttle and adjust needles as necessary. At least your conscious of the issues and willing to make changes...that's enough to keep our ass out of trouble!