Use the 5v. I used 5v on my ms3x, as directed by diyautotune.

My wiring is all posted here (and the 12v ref is on this diagram as well, but NOT what I did)

My link:
http://www.forabodiesonly.com/mopar/threads/how-to-megasquirt-your-3g-hemi.226125/

Diyautotune link:
https://www.diyautotune.com/support/tech/install/chrysler-dodge/megasquirt-your-hemi/

Who did you buy from? What did they say?

-'02 Dodge Viper Ex-World Challenge racecar
-'73 Duster, 6.1 based 392 hilborn hemi, tko600, full floater rear 9", Hellwig custom bars, viper brakes, built for road course