Also, if PIN 46 shows continuity to PIN 48,then the computer would be trying to go into test mode. So you need make sure the PINs you are testing, are the actuall PIN you think you are testing.
Did you try unplugging the O2 harness like I suggested?
No we didn't disconnect the 02 harness, I forgot to do that. One of the first things we did when we started looking into this problem was disconnect the maf sensor. The car seemed to idle ok, so it shows the computer can go into limp mode.
Do you still have the jumper wire from the signal return to the STI hooked up at the codes test port? Continuity from PIN 46 to 48 needs to chased down. And if you have continuity from 46 to 26 then some where there is a short on either the Map/bp sensor,EVP, or TPS wiring.