Yes mis-aligning that connector can cause lots of problems.
What I would do if I were you is:
1) Pull instrument cluster
2) Remove the fuel/oil/coolant pod.
3) There should be pin numbers silk screened on the otherside of the circuit board.
4) Use these to mark pins on the back of the circuit board where the connector goes.
5) Re-install pods.
6) Re-align pins based on the numbers you wrote on back.
You can vaguely see the numbers in this photo, they are a bit out of focus.
http://i.imgur.com/1QbabaW.jpg
If you orient that connector wrong it MAY damage something. I am not sure. I dont remember the pin out of it so if by mis-aligning the connector you've applied a voltage to something that should not have received that voltage..then maybe something got damaged.
I do service work on the instrument clusters so if you would like, you can pull the cluster and send it to me. I can check out it for you, etc.