Ive had my 04 since 49k miles and I love every second of being ProTuned.
Some BOV's work better than others, but isnt needed unless you are running 23ish psi. The stocker starts to leak around that. Modding your injectors is okay as long as you have them flow tested. STI Pinks is a great alternative.
The thing that sucks about the 04 is, is that its slow until you get some form of Engine Management on it. Trust me , youll love your decision. Ive put around 20k hard miles on mine as Stage II and have had no issues. It runs better than the first day I bought her. Im about to upgrade my turbo as well.