Yea, if it came with it, it be a hell of a deal. Maybe the 6000 one comes with more? Idk....but injectors cost from 500-1000, depending on what you get, probably wouldn't need much bigger ones depending on the level of boost you planning on running.
Tune, depends on who you go with, but dyno tunes are usually in the 400+ range...
So I say the whipple is would be the best choice, the cost would more than make up for any fabbing you would have to do.
Also, if you haven't already, look at Hotrado (i think that's right), he has a supercharger on his 5.3
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