MacBook – Replace hard drive whilst saving installed software

All you need to do is plug in your iPhone 4 into the Mac, and depending on your setup, iTunes should start backing it up. The Mac isn't actually a requirement here, if you set up the iPhone 4 with iTunes on a PC, you can do the same there.

When you get your iPhone 4S, and plug it into the computer, it will ask you if you would like to set up the phone as a new phone, or use a backup from a previous device, like the iPhone 4. Say yes - to use the backup - and it should set up the 4S just like your 4.

With iOS 5, iCloud actually will do part of this for you as well. If your iPhone 4 is already backing up to iCloud (instead of iTunes), when you set up iCloud on the 4S, it may ask you if you want to set it up using the previous backup. This is exactly how I migrated my wife's iPhone 4 to a 4S when she got it.

Since only one drive gives you a flashing ? when mounted internally, you've pretty much ruled out hardware failure of the controller and the cabling.

I would first try booting into the start up manager by holding the option key with the problematic drive on the internal bus. The ? can come up when the startup disk settings in NVRAM don't match the drive, but if any drive connected is bootable, it should show when you boot with option held down.

Your next step after making sure it's not startup disk settings would be to erase that drive entirely and try reinstalling OS X onto it. You could flip a coin and decide to do the installation internally or externally.