Check out the main relay.
If ground side switched then two hot and one ground
The fourth is the Switch.

Wait, did you say that the fuse was not getting 12 volts?

 

I dont understand what your trying to say? The main relay has 7 or 8 pins on it and is located next to the ecu. And correct in the under hood fuse box I wasn't getting 12 volts to the ecu fuse when hooked to a multimeter. But the power coming into the fuse box is 12v so idk what's going on.

 

I forget that Honda has a different type of main relay.
There is actually two relays inside
The ignition switch controls the power to turn on the relay to power the ECU
And then ECU controls the ground side switching energize the relay to power the fuel pump
So you have no power to the ECU or fuse
Which is why there is no check engine light which first turning the key to the "ON" position
Which tells me that the relay is suspect.

The main relay has 8 pins of which pin number 6 is not used
Pin 1 is to battery
Pin 2 is to ground
Pin 3 is to ECU power up
Pin 4 is to st. switch
Pin 5 is to Ignition switch
Pin 6 is not used
Pin 7 is to fuel pump
Pin 8 is to ECU control fuel pump

There are plenty of videos on youtube about the main relay issues.
Would do a little more testing before deciding to repair or replace part.
Good luck

 

If I remember right my number 4 pin is the one that isn't used cause I did pull it off to have a look at it. But I'll definitely look further into it just seems weird how it would go bad after I just changed the motor and wanted to do the initial start of said motor when it worked on old motor two days prior.

 

Yeah, it is strange. So this is why I suggest to look deeper into this before changing any parts.
Think pin 4 can just hang according to the schematic for the main relay. Not sure.
But, it should have 12 volts when trying to start engine

According to the internet, the main relay has known issues with solder joints cracking
However, since connectors were taken off and put back together, I tend to believe some pins might have bent.
But, I don't know. Please let us know if you find the problem.

 

I never removed the harness from the ecu just the engine. I'll be looking into it deeper today after work I've done many of these swaps and have never had this problem before so hoping to figure it out asap.