Jgorm, have you ever tuned a stand alone ECU from scratch? For a one-off setup like a custom turbo kit on an engine/trans combo that nobody makes an off-the-shelf tune for? Yeah, 50 hours seems like a lot, but it's realistic for a GOOD street tune. Minimum would be 24 hours, realistically. I'm not talking about something like a Diablo, which has limited capability. I'm talking about an AEM stand-alone ECU, and full custom tuning.
To be honest, I haven't gotten to play with the new Diablo tuner for the JK yet, but I can assure you that it can't even begin to compare with the features a custom ECU bring to the table.
Also, a high-flow throttle body is a waste of money for high boost- they're more important for NA (Naturally Aspirated- in other words, no turbo, nitrous, etc.), as those applications see greater gains from de-restricted air pathways.
As for failure and issues, I don't see how you could make that claim- it's a hunk of metal. I've worked with many over-bored TB's over the years (mostly on Honda/Acura, and Mustang/Camaro applications) and never had one fail- either the homespun kind (had a great guy in central FL who had a 3-day turnaround, including shipping, for $100! Loved him
), or the off-the-shelf kind. Had throttle return springs fail, but those were often stock parts, re-used.
As always, my disclaimer- I'm not personally crapping on you. Just stating what I've seen in my experience- Mark W.