Need help to setup EmonTX 3 Phase based monitoring

Welcome, Charles.

You were looking in the wrong place. The guides generally only talk about the UK single phase system. You need to follow exactly the calibration instructions in the comments at the top of the 3-phase sketch. You are seeing wrong values because you have the three phases mixed up.

The reference is the voltage input, and the 3 ct’s must be on the correct phases in relation to that.

First, you must find which phase the a.c. adapter is on. Everything depends on that. I’ve never done this, but it should work. Ignore CT2 & CT3. Switch off everything in your house. Connect a high-powered electric heater to that outlet as well as the a.c. adapter. Put CT1 on each phase in turn until you read the correct power (approximately - within 10% is OK). That will tell you the phase that the outlet is on. From now on, to the sketch, that is Phase 1.

It does not matter whether that is the brown, black or grey phase at your meter, but the other two ct’s must follow in the correct sequence. To the sketch, these are all the same:
a.c adapter & CT1: brown, CT2: black, CT3: grey
a.c adapter & CT1: black, CT2: grey, CT3: brown
a.c adapter & CT1: grey, CT2: brown, CT3: black.

Now, with only the high-powered electric heater still connected to that phase, do the “calibrate on a single phase only” procedure in the note (in the comments in the sketch). When you have done that, put CT2 onto the next phase in the sequence and CT3 on the last one. Then you should have “sensible” readings on all three phases.