Chosen Solution

Swapped out HDD for OWC Mercury Extreme Pro 6G SSD. With a clean install. SSD installed internally = terrible performanceHDD installed internally = normal performanceSSD installed externally = normal USB performanceHDD installed externally = normal USB performance All I can conclude is that there is some issue with the SATA cable or interface? Has anyone experienced this (and did a cable replacement fix it)?

Replace the HD SATA cable! This is a common issue in this series. Here’s the IFIXIT guide: MacBook Pro 13" Unibody Early 2011 Hard Drive Cable Replacement and here’s the part you’ll need: MacBook Pro 13" Unibody (Mid 2012) Hard Drive Cable and yes! this is a newer better version of the cable used in the 2012 model. I also place electricians tape on the uppercase where the cable crosses over to help protect the cable also don’t over bend the corner bends as the foil wires inside are fragile! You’ll also want to wipe the drive and reinstall the OS and restore your backup as you may have some corruptions.