.... With the key off voltage at ems relay is 12.6 on the 2 big wires and 11.7 on small yellow wire ground reads 11.7mv,
with key on readings are the same and with kill switch hit to off no changes same volts,
That suggests that the ECU is enabling the Relay to be ON (via that Yellow/Grey wire) even when the Ignition Circuit is not powered!
Is this immediately after turning ignition key off, or do you get the same thing if you just check it cold (without attempting to turn it on again) maybe 15 mins (at least) later?
What you need to do is check to see what the voltage is on the ignition circuit -
Check voltage at Fuse #5*
a) with key off - Kill-Run in Kill
b) with key on - Kill-Run still in Kill
c) With Key on, Kill-Run in Run
d) with Key OFF, Kill-Run in Kill
* Note that you do not have to remove the fuse - touch the meter positive probe to one of the metal tabs on the top of the fuse.
This will help to determine if you have a key-switch problem (or some other short on the ignition circuit) or a faulty ECU.
To add to this question key off volts 12.70 key on 12.43 30 seconds 12.34 and 1 minute 12.34,
Can you confirm that the headlight is on when you take the key-on measurements?
(If so that is actually quite good - I would say surprisingly good actually)