Update 1-22-17
Talked to Gadget about the issue, and he hooked me up with Scott from Itronix who has been a big help.
The no start was my fault, and I have nothing but ignorance to blame. I previouzly has a MK1 kit installed and had intermittent problems that I never found the source of. To try and eliminate the possibility that it was my ECU, I bought one from another 06 X-Runner and installed it at the same time as the MK3 system.
Scott informed me that each ECU is coded to 1 specific vehicle. You can't simply swap them. I had no idea.
After switching back to the original ECU, the truck fired up for the first time in a week, but was running rough. I had cylinder 4 misfiring, so I took the brand new plug out, and it was black from all the attempted starts and wrong computer, so I cleaned it with brake cleaner and reinstalled. It cranked back up and ran smoother, but still not perfect.
I discovered a vaccum leak at one of the t fittigs that smoothed it out even more.
The truck is running, but still seems to be misfiring some. I'm going to clean and reinstall the other 5 plugs and see how she runs then.
Thanks to Gadget and Scott for the technical support. Hopefully I can get it completely smoothed out.
I've done a couple WOT data logs, and it pulls pretty hard! If we can get it all smoothed out, I'll be really happy with the power level.