Lets start with contacts and see what you have. I think we can sort this out if you haven't proceeded too far.
I think if you check closely in contacts you should see "Contacts iCloud", "On My Mac", and maybe on My Mac 2.
They will be consolidated in the iCloud but should still be separate contact lists for each device that provided contacts.
Is that what you see?
Just to expand on this a bit...
Make sure to click on "View" on the menu bar at the top of your screen, and "Groups" is selected.
When signing into icloud, if "merge" is selected for contacts, you will only see "All Contacts". If this is the case, then it cannot be undone easily. You'll have to pick through and manually delete what you want removed. Unless you have a backup of some sort prior to logging into icloud?