I'm sure it's possible to fix your install... you/we need just a couple of time.
Do you have time / patience to fix it ?
How are your linux skills ?
First of all: you'll have problems with user/groups and permissions. Files where copied with WRONG USER and GROUP IDs and are a REALLY MESSY thing.
So here is my tip:
1) let's start by one SHARE: copy each file/directory where it should be and change SOMETHING (anything even a description) on web interface and save.
It should redo all permissions.
Test if this share is ok. If not you can use a shell script to fix it. I can provide it for you later.
2) if this path works... repeat for each SHARE.
3) for user directories, it's just a matter of fix permissions using a shell script (I can provide you).
it's something like: "chown -R X:Y .*" and later change ".*" to "*""
Where X:Y are the username and account.
If you need assistance with this, post and "ls -la" of one directory of user and I'll help you.
BTW: This is the REALLY HARD way to move content between servers: Affa is the easy way!

Regards,
Jáder