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You only need to save the config folder from the old SSD that is located in the "user name" folder so should be EMC2 or LinuxCNC and inside is the "configs" folder so copy that.
You can try changing the SATA cable as those can cause such issues, look for cracks in the shielding near connectors and if you see any = change cable. And if there other SATA cables plugged into the mainboard but not used, unplug those.
The strange thing is, there is no Ubuntu 12.04 with LinuxCNC officially, but there is a Debian Wheezy ISO with the same kernel.