If you want the engine to be noisier then get a CAI if you don't then stick with your stock airbox. I put an Airaid on and at certain RPMs it is loud as hell. Like conversation stopping loud with the windows rolled up. The TRD is not as loud but costs the most.
I don't really think I lost anything low end but cant really tell anywhere else in the RPM band. It's not going to give you that hang on to your @SS pull over what you already have.
As for keeping stock pipe and putting in a magnaflow, this is fine. Not an issue at all. Keeping the same size exhaust is usually a pretty good thing if you aren't redoing the entire exhaust from the heads back.
Pick your tip, there are plenty out there.
Rolling Big Power - Diesel Performance, check
ebay, Toyota has them. Check with the muffler shop that is going to put your magnaflow on, I'm sure they have some to choose from. Pick what you like.