Would highly suggest putting a 3" down pipe on it to replace the factory one, any of us sponsors on here can get them!
after that I would remove the factory intake and stick a filter on there from your local auto parts. Give them the part number 6637 and they should be able to look it up. Let that filter just sit in the factory location, no need for a box around it.
If you are looking to add a little power, a set of gauges and a TS 6 position chip with custom tunes would certainly be my next move. Tranny work and injectors soon to follow depending how much power you are looking for!
PM if you have any questions, there is a lot to learn and plenty of good people here to help you out!