On the cheap:
• Find an LTR tube for the stock airbox (this will fix the most restricted part of this bike. which is the airbox tube that literally has a kink as it goes around the rear shock.)
along with a mesh lid like this one
<-- I've seen a few others as well.
You will probably want to put a breather filter on the crank breather line if you go with the LTR tube.
This modification to the air box is by no means hard to do and will free up a lot of power. (easily done for >$100)
• Find a used (3 Button) Dobeck fuel controller. LEXX, motosport.. on and on Very easy to setup but will leave some power on the table that a properly tunes PC3 with a good map would have.
(I think there is one for sale on the kfx450hq website for $80 shipped)
• Buy a used full exhaust. Also one on kfx450hq for $300
Total > $500
Other options would be
• PC3 (plenty of maps for this floating around)
• PCV with autotune
As far as the FCI I have had no experience but everyone seems to love it. I just bought a CFM box which I really like. Has a lid and a drain hole.
My suggestion would be to pick a budget and go from there. But if you want to do it on the cheap I don't think you can do it for much less that what I have come up with.