Chosen Solution
I bought the second HD kit just after purchasing the Mac in 2011 and installed a 1TB second drive. Ended up removing that drive and the stock drive as well and installing an 80GB SDD that worked perfectly until I ran out of space due to the data files for a massive iTunes library stored on a 4TB external drive. I installed a second 80GB SSD as a user drive to solve the space problem and used the drive utility to combine the original 80GB back into one partition. When I installed the OS the new drive would not show up in any utility or the terminal. I finally installed the OS on the new SSD and both drives were available, however the online reinstall would only install lion not mountain lion. When I upgraded to mountain lion I would get a grey screen only able to safe boot. On safe boot all drives are available. I switched back to installing the OS on the original drive but again lost the new SDD. Sorry for the long winded description as I saw no other problem here that exactly matched this. Also the 2 SDD and one external HDD is the configuration I plan to use so please no answers suggesting different drives or configurations unless you know my configuration will not work.
I would recommend going to the Genius Bar at an Apple Store and ask them if they know of any issues with a dual SSD setup with Mountain Lion. As you do have Lion working maybe you’ll need to stick with that until Mavericks comes out. I would make sure the EFI is up to date in any case: EFI & SMC firmware updates for Intel-based Macs. Please let us know what you find out.
Make sure the new drive is initialized. Sometimes they aren’t and until it is nothing will see the drive. Not much of an Apple guy but I know from lot’s of experience with Western Digital I would have to hook the drive up to a windows machine with Hard Drive USB reader and use the Disc Management app to initialize the partition on the drive. May be the case you are facing here. Once done I then had no issue installing to the drive etc. I know you mention that the OS was able to see the drive at one point. I would just make sure that the drive is showing up correctly and that the partition is fully initialized. Can be done with a $25 hard drive reader and any computer system. Plus it is just a handy thing to have.
I read up on the Genius aspect and called the support dest at the local Apple Store, theire reply was the same as the web site that they do not support other then apple installed drives in the Mac Mini.
I am not sure what you are trying to do, but I think from what I read, you are trying to build a 2 drive RAID. OS X 10.6 was the last version that will install on a RAID. If I remember correctly, I think it had to do with the new hidden recovery partition they started using with OS X 10.7. Basically, you get your OS X 10.6 installer and boot from the installer (DVD or Thumb drive). Once you’re booted up, you can switch to Disk Utility and create your RAID 0 or 1. Quit Disk Utility and install OS X 10.6 normally onto your newly created RAID volume. Once you’re done, you can boot up and copy OS X 10.7 installer into the Applications Folder and double click to update to 10.7. You will not have the hidden recovery partition doing this. You can continue on with OS X 10.8 the same way. I am assuming OS X 10.9 will update as well. I have been running Mac Pros in my office and my personal Macbook Pro this way with dual SSDs. I didn’t trust Time Machine back in the days, so the office Mac Pros had a mirrored RAID set which worked great. My Macbook Pro had a striped RAID set with dual SSDs, but I was using Time Machine to backup. Also, if I remember correctly, running any current version of OS X 10.7 or newer on a RAID volume will not allow you to use some of the features of iCloud because they require the hidden recovery partition. I think the features were Back to My Mac and Find My Mac. You will have to check this because its been a while since I looked at it. I just picked up one last non-retina Macbook Pro and I will be RAIDing the dual SSDs this weekend. Hopefully to OS X 10.9. ;) I will be setting up the striped RAID between two SSDs and then installing OS X 10.6. I will try to update directly to OS X 10.9 and see if it will go. It will save a lot of time if it works. I think Fusion Drive was supposed to replace RAID support to allow for the hidden recovery partition. New technology and more storage for cheap. Hope this helps.
