edit: someone logged into mud on my PC!!! This is not AuburnFJsexy...
My 91 came with a K&N filter, otherwise I would not have it. I think it makes no difference and I keep it clean. I had my exhaust completely redone, replaced the 2 OEM cats with 1 catco hi-flow and borla muffler with 2.5" pipes all in the stock location, in fact the tail pipe is tucked better than stock. Note: I don't have the complete borla system, as I think the tailpipe is in a terrible place and could be crushed. My exhaust does make a difference. I roll on 35's with stock gears, and it could be a slow beast, but I guess I know how to drive it because I have dropped FZJ's going up winding hills (I realize that's the driver and not the truck).
Anyway, stop worrying about what may make it faster or give more horsepower, since that's not what it is for. Because trying to make the 3FE have more horsepower is lke trying to make a civic/neon a sports car... it ain't gonna happen.