Convert case-sensitive HDD to journaled insensitive

The correct answer (after several days of experimentation) was to remove all ambiguously named files that would have a conflict. Then using another admin user, restore the original user using migration assistant. If you don't remove ambiguously named files, migration assistant will move what it can and then fail at some point giving no indication that it actually failed. You'll be without data and you won't know what.

I believe the issue to be that the controller is still SATA III for the optical bay, yet the connector is a SATA II type, as is the cable. So if you try and place a SATA III enabled drive in the optical bay, it will try and negotiate at SATA III speed (6G). This creates an issue as the cable is not setup for this and the crosstalk, and very low SNR at that speed causes many errors. I got my Seagate Momentus SSHD disk drive working somewhat in the optical bay by wrapping it and the short cable in tin foil, making it a good ground to the chassis, but it still had loads of errors on it. I ended up putting a SATA II disk in which works. My Macbook is a 2012 13in with an 2.9GHz i7 in it. This shows both connectors as 7 series Intel Chipset, both of them are supported for 6G, yet the optical drive is negotiated as 3G (SATA II). My Samsung SSD in the HDD bay, is negotiated as the full 6G.

Have a check in system profiler to see what supported speeds and negotiated speeds you are seeing for your controllers. There seems to be a lot of conflicting information about what model supports what, but it makes sense that the controllers are the same type on the main board for the particular chipset being used. The connectors are different though.

I was hoping there would be a hard disk that you can force SATA II on, or some way of enforcing the controller to only ever negotiate up to 3G, but thus far haven't had any luck :-(

Hope that helps demystify the core issue at stake here somewhat.