after i emailed them a message in the bios with the sata 3
First of all, SATA drives do not need to be configured as Master or Slave.
Secondly, did you try my suggestion above with regards to repairing the MBR ?
Finally, if they send you the HDD, then it will probably be blank and you will have to re-install windows.
Not forgetting you will also lose any manufactures backup/recover software on the drive.
So the best think to do is to "Clone" your old drive, then re-install the clone file onto the new HDD.
If you can still access your old drive, then just insert the new drive into the PC and clone it over.
Personally I would take it back to the shop and let them do it.