You do have it wrong.
Looking at your pics and going from the new unit wiring list, the correct way would be:
Bundle 1 (this is the alternator output and the regulator circuit input power)
White/ Red to Battery Positive - This goes directly to battery "+" or to the red/white wire on the old rectifier plug. You have it connected to the alternator field coil wire on the old regulator connections (wrong).
Green to Battery Negative - should go directly to battery "-" or to a solid ground point, you have it to the old regulator green wire. not entirely wrong but it should go straight to the battery or frame.
Black to 12v source after switch is turned on - This one you got right!
Bundle 2 (this is to the alternator coils only)
3 Yellow to Stator- 3 phase output coils - you have these right, yellow to yellow.
Black to One side of field or brush 1 - see below
White to other side of field or brush 2 - see below
The white wires are for the alternator field coil. This coil has two wires, one is the white wire at the regulator (you have the new red/white one connected to it). The other one shows up on the engine connector but is grounded in the harness, I don't know exactly where. The stock regulator supplies "+" voltage to the white regulator wire and the coil is powered to ground. I don't know how the new regulator works (it could control either positive or negative on the coil), but Cycle-X seems to want both coil wires without any grounding so that's what you should do, so you have to find the other field coil wire. It does come through the engine connector, I think the coil is on two white wires there (the only white wires). You may be able to find where it goes to ground and, after disconnecting that, extend it to where your reg/rect is. Or run a new wire to the engine connector, it uses spade connectors that can be removed from the shell so a new wire can be carefully soldered on.
Once you have both connected to the new white wires and the others corrected, you're good to go.
