Is your DP catted or catless? Are there any inspection issues with going catless? We have emissions inspections in my state.
Catted, we have OBD2 inspections here and they can look closer and see if you have a cat. I'm not a big fan of the obnoxious smell of the catless either.
If you are super worried about running an aftermarket downpipe you can keep the stock one, do the intercooler and get a custom tune.
Depends on what you want as far as the intake and exhaust...do you want the sound or are you more worried about performance? The injen intake is loud, but it sucks in hot air and heat soaks pretty bad. MBRP exhaust is fair priced and loud but drones pretty bad (especially with a aftermarket DP)
You can always go for stage 3 and then go pro tune later if you decide it isn't enough. My plan is to eventually get the lifetime tune from Tune+, you pay once and can get a re-tune every time you upgrade something, even if you go BT later.
As far as the hard pipe for the hot side. I have one, but I can't tell any difference in performance or sound (maybe I can't hear it over my droning ass exhaust). I've read that the stock pipe flows good enough for BT. But as cheap as the MBRP hot side pipe is, you might as well get it.
My advice to you, do the research and find out what will work for you. We can argue back and forth on here and get no where, hear say is just that. Like I said the J-Line and depo racing DP work for stage 3 on my car. Yours may be different. Good luck with whatever you do.