Couple of things to check.
In your description of the plugs when fitted together,what colours matched with each
other was wrong.
are they all now matching the photographs I put on for you and my list of which cable
matched the other

RE your Auxiliary module connections they look Ok.
What I have noticed in the Electronics Modules Manual,Page 14 and 15,the Blue and brown
cables on the left hand side are shown different ways.
Page 14 shows Blue Brown and page 15 shows Brown Blue.
Mine is like on page 15 and yours is like on page 14.
Dont know if this would make a difference any way because both of those go to the
elevation motor,but you could try a quick swap to see.
If all the colours deffinately match up,which side of the loom plugs did you remove
the connections from

If it was the Limit side you could try disconnecting the plug and check each connection
to the 7 black and green/yellow with your multimeter,to check for a good connection.
Last thing I can think of is that to change the direction of the Elevation motor would
need a Relay.
So just like the relay in your Speed controler it could have a stuck contct,so take the
cover off your auxiliary and use your magic finger for a quick tap of any relay box you
can see.
Because it worked for you on your bench test before altering the connections,it must
still be the connections or the relay.
You must have altered something back right to get the one limit working.
Keep going Mick and let me know how you get on
Cheers
Phil