I haven't changed from the stock throttle body, and from what I've been reading you have to really be pulling some air for a bigger one to be an advantage. I don't know if that would complement a stage 1 well or not.
I wouldn't think a stage 1 cam would be a big enough difference to throw off the stock ECU, but I'm sure a tune wouldn't hurt anything. What obd are you running?
I'd recommend spending some time in the Naturally Aspirated forum and looking around at what those guys are using. If I remember there's a really good cam write-up stickied in there, as well as a general FAQ one. And honestly you'll probably find people with more experience who could better advise you on this. I'm still at the stage where I'm wondering about the same sort of things because I haven't tried them first hand yet.
Sounds like you're already doing this, but I'd keep searching and reading. My first mod was a closer-geared tranny, a stage 1 clutch, and a slightly lighter flywheel and that made more difference than anything intake or exhaust-wise. What are you running now?