Possible bad 2006 Tundra 4.7 ECU

Two years ago I put a Hewett Tech Gen II Module into my 2006 Tundra 4.7 to remedy a faulty SAIS system. The module has worked fine up until 6 months ago when I started getting a P1613 code. I recently installed a Hewett bypass module to correct this problem, after instillation the truck gave 7 error codes and cranked but will not start. Hewett tells me that the wire colors for the bypass are reversed. I Rewired to the proper orientation and the truck still cranks and will not start with the same error codes. P0113, In Air Hi, 0118 Coolant hi, 0123 Throttle Pos, 0453 Evap, 1613 SAIS Driver, 2135 Throttle, 2433 SAIS.
I have disconnected the battery numerous times, and cleared the codes with my code reader many times and the codes keep coming back.
Is there another way to reset the ECU that I am missing.
Any thoughts on if I need a reman. ECU?
I am in contact with Hewett service but they have not been too helpful.
Thanks for any help.

 

Info stolen from @Shifty' here

Hewitt Tech makes a Gen1 and Gen2 kit, the latter requires some soldering near the ECU, behind the glovebox, 3 wires if I recall, the Gen2 seems to have the most 'random codes afterward' issues and I can't speak to the Rutech. This thread discusses a DIY kit which is basically covering what Rutech and the Hewitt Gen1 are doing. This is some documentation if you're a DIY'er and don't mind pulling together the parts to make your own solution cheaper, but I don't recall if it'll deal with the valves or not.

Anyway, it's worth reading that last link with the DIY info. IIRC, it explains the system so you at least understand what's going on.

 

Thank you Black Mamba for the information.
In the end I untaped all the connections that I mad for the Hewett bypass units and found that a black/ white wire had managed to break loose and hid itself in the wire bundle. I reconnected the wire, cleared the codes, the truck now starts and runs fine. No more codes good for another 165,000 miles, I hope. To anyone doing this modification the wires are very thin and easy to break, be careful.

 

I'm actually shocked Hewitt wasn't more responsive. Several people have come here saying they were more than helpful. They've posted here answering questions for owners having issues.