Welcome to the board.
I have a stock FT with the OEM head-pipes & a straight through glass-pack type of muffler. I removed the air box & used an oiled foam UNI filter. I had already performed the jetting swap like is described in the FT Ascot Essentials, but I still need to add more fuel. The engine breaks up a bit in the 3800-4200 RPM range if I recall correctly. You will also need a small breather filter for the crankcase breather. I used one of those small generic K&N type of filters with a mounting screw in the top. I mounted this filter from one of the original air-box mounts at the top left frame rail & then ran a hose from the crankcase breather port to the filter. I'll post a pic or two below of the crankcase breather.
When it comes to filters, I don't trust the K&N screen & gauze type of filters. They allow fine dust to pass through & sucked into the intake tract. I much prefer the oiled foam filters like the UNI.
You can easily run a pod type of filter, but you will need to adjust your jetting. If you remove your air-box, you might lose your battery mount & one of the side panel mounts. I can't remember for sure on that.
Good luck & please let us know what you find out.
J.