Even though the situation seems complex, the solution may be simple. I have an un modded 2000 Echo, I had a CEL on throwing misfires in the plugs. Meh, I think, a simple change of the plugs, and the CEL light goes away. (I even talked about it HERE but I get in and start her up, and I still have a CEL light Ok, so off to auto zone I go, there are no codes being thrown. I go home, and scour the forums at Echofans, and it seems to be that I need to reset the electric system by simply disconnecting the battery for a few minutes. This resets the CEL, among other things like the MAF and VVTi solenoids and computer components, and the CEL went away with some simple trouble shooting.
Expect the car to run like ass for the first 15-20 miles warm until the computers can get their comparitive readings and you should be in business.
IF this doesnt work, then I would call upon Wraith or Toytech as he has had the blitz turbo and very well may have had experience in a similar problem