You really can't go wrong with either tune. Since you're not doing extensive mods, it really comes down to which one appeals to you. JB4 has great auto-tuning abilities, E85 support, on-the-fly controls and out of the box meth support if you want to add it. Biggest downside is obviously installation and hardware sitting in your ECU box.
COBB is stupidly simple to install, no hardware left in your car and getting a lot of focus lately around E85, race, meth and ATR maps. Biggest downside is they don't have auto-tuning so you're stuck with a few maps based on your mods. And they are especially conservative with CA91 gas. To get the absolute best out of it, you'd have to consider a custom tune, but you're local to SoCal COBB, so that's a plus.
For intake, just get a DCI. If you absolutely have to reinstall the stock, it doesn't take that long, it's not like downpipes or exhaust. Another option is Injen which is CARB approved.
For exhaust, if you're so worried about smog that it's impacting your decision on intakes, I'm not sure what you think you will do here. Anything except a muffler won't pass. Almost all "cat-backs" still remove the secondary cats on our cars.