2001 air issue

Hi, new to the forum, looking for some help with my Trail Boss.
I purchased two 2001 Trail Boss from a guy that had them in storage for about 3 years. He kept them in good shape, fogging them and turning them over. My problem is one of them will not take throttle, it starts to bog out at about half throttle. The only difference between them is one is a post 12/11/00 and the other is pre 12/11/00. The only thing that sticks out to me is the air box style. The post ATV has a smaller K&N filter, and air intake . I have swapped everything between the two and it seems to come down to the air box. If I put the pre12/11/00 air box on either one it runs fine. If I put the post on it, I need to take the cover off for the thing to run well. I am at a loss. Not ready to drop a hundred bucks on a pre 12/11/00 air box and filter if I can help it.
Any help at all would be appreciated.
Thanks
Mike