Ok, final update on the saga.
Looks like the "findings" were a non issue, think the local shop was just trying to be thorough to CYA. I appreciate their diligence, but it probably made me more paranoid than usual.
ECGS was a good joint to deal with. I would go back through them in the future, with one and only one caveat. If the vehicle is a daily driver that you need to minimize downtime for, it's probably not the right service to use unless you are on the east coast due to shipping times to correct issues that may arise. In that situation, I would likely use a local gear shop that can turn around the job faster. Although I think I was one of the rare people to end up with a set of gears that bothered them, I would basically factor "how stressed am I going to be if I need to pull the diffs again" into the calculation. For a car you can leave in the garage for a week, this is a total non issue.
With that said, the quality of work from ecgs was solid, they do have good customer service, and they do work to make things right by their customer.
Few lessons learned:
For 456 gears, you will need a 373 and down carrier since the gears are only available in "thick". This means that if you put a e locker in, you will need a different e locker if you decide to go back to stock since our stock gears are 391.
I"m very noise sensitive, so I probably should've stuck with stock gears, lol. If a bit more noise doesn't bother you, or if you roll with M/T or R/T tires, you're probably golden

even if they do whine.
The 456 ratio is $$$$$, even on stock tires. I really wish it would've worked out, Lexus really should've geared the vehicle like this from the factory.