How complete is either system? (down to the fuel lines?)
If neither of them is that complete, I'd probably look at getting a TPI setup yourself and going from there. Last I saw a complete one, $500 was the going rate. Even with new injectors and a couple of sensors (if needed) you'll be under $1000. New tank, lines, pump, etc., you'd still be under that $2300 figure. (edit: re-read your sig...TPI is going to choke your motor)
I'm not saying the pro-flow isn't worth it, I don't know enough about it. But typically you pay a lot for a "nice looking" system that isn't any more functional than what you could find yourself. You also pay for the perceived "plug and play", which really equates to not understanding how it all ties together, especially for troubleshooting.
Factory systems are probably going to be easier to find parts for if you break down somewhere, but at the same time, I'd be surprised if Edelbrock recreated the wheel. They probably picked factory components (not necessarily only GM) that do what they needed them to do, and built the system up from those.
Of course, TPI is also limited for upper end, and as it comes hardware wise, is undersized for a healthy 350. You start talking aftermarket intakes, fuel rails, etc., the cost climbs significantly for TPI.
You don't HAVE to burn your own chips for it, you could probably have someone like tbichips.com do it, it's the same process TBI/TPI, although obviously they are different systems, he can likely do both.