OK. We're being more thorough about documenting all the little extra pieces needed to get it working this time. The I-5 was bought pretty much as a complete pull, so we cheated a bit on that one. The I-6 came as a long block+ so we're needing to piece it together more.
If there's a local tuner shop, they're likely to have HP Tuners-- As I mentioned, the 'tune' was pretty easy in that we just wanted the stock tune (we're running factory cats, intake, exhaust, etcc) so the majority of it was just turning un-needed stuff off like VATS, CAN bus interfaces, error codes for stuff that doesn't exist in an FJ swap (like radio/XM/OnStar interfaces, etc). I'm sure a friendly local shop wouldn't charge much just to hook it up and un-tick the boxes.
Since taking delivery on my I-5 it's not been hooked up to HP Tuners again. Runs great, idles great, starts great- at sea level or 9000 feet.