Having performance issues after cloning drive.

You likely have two issues here the first is cloning is not such a good idea! Many cloning apps don't setup the recovery partition and you likely need to apply some firmware updates which only happen when you do a full OS install.

The second issue is as you described your HD SATA cable is likely worn. This is a common aliment as the uppercase surface is a bit rough and can damage the cable.

First I would replace the cable following this IFIXIT guide: Remplacement de la nappe du disque dur du MacBook Pro 13" Unibody mi-2012 and here is the part you'll need: MacBook Pro 13" Unibody (Mid 2012) Hard Drive Cable. Where the cable crosses the upper cable place a strip of electricians tape to help protect the new cable.

You'll need to make an OS installer to first delete the current partitions so you can re-do them using the OS installer drive to boot up your system. Here's the guide you need to follow: How to create a bootable macOS Sierra installer drive Now before you jump on me I don't recommend going with High Sierra with SATA based SSD's! Apple still has some issues with queueing. High Sierra was tuned for PCIe/NVMe SSD's. So please do your self a favor stick with Sierra until the next release this fall which is when I'm hoping they fix things with APFS.

OK, You've setup your SSD and installed a fresh OS on it now we want to bring your stuff over. This is where you can use Migration Assistant to move the user accounts, apps & user data from your old drive. You want to use Migration as it will fix and damaged files from your bad cable you had with your HDD.

Next time use time machine backup