Everyone I know personally has had nothing but problems with their 3.0s and 3.8s; it was a mix of Gen 5s and 6s. One of them has gone through 6x Whipple 3.8s in 1500 miles of abusive driving. Last time I spoke with HHP, a few months ago, they said the Gen 6 Whipple 3.0s seemed more reliable, but they still needed to determine the 3.8s. I was really hoping to hear they resolved the problems since the 3.8 seemed like the best option for my 426.
If you're thinking about switching, I have yet to hear any negative experiences with the Kong 2650. They run a bit hotter than the Whipples due to it being a Roots-style blower while reusing the factory intercooler bricks. I have a ported Kong 2650 with a 2.5" upper and 10% overdrive lower, making 21-22psi on my motor combo. I'll be dropping down to a 2.35" as soon as it arrives in the mail.