I just completed engine and dash with an M&H harness and with the exception of the convertible courtesy light, everything connected and lined up correctly.
You're past that point I'd say, but having the wiring diagram and labeling everything before removal... Then doing a side by side layout... Labeling the new harness before going at it is essential.
Edit to add. This is on a 64 Valiant
Sorry, I know good ideas after the fact are no help.