'Macintosh HD' not bootable anymore after installing Yosemite on a second disk
Open up Terminal.app, in /Applications/Utilities, and enter the following:

diskutil list


It should show both of your drives and give you information about partitions. You may also want to try:

diskutil cs list


On Yosemite, some of the volumes are defaulting to Core Storage, which can span multiple drives. I'm not saying you did this, in fact I rather doubt, or at least hope you didn't, was inadvertently convert both drives to a single, huge volume that's really two drives.

I use Scannerz and it comes with another drive management tool called Phoenix. In their release notes for the Yosemite version they said that some systems earlier than Mavericks may not fully be able to see or manipulate files on a Yosemite volume, but a Yosemite volume is supposed to see and be able to manipulate. In other words, if you boot from, say Mountain Lion, you may not be able to do what you want to on a Yosemite volume. I know this is true for stuff in the low level system directories, but I'm not sure it effects user volumes. Maybe they'll put something about this on their web site, but then again, maybe not. I'm not convinced this isn't a Yosemite bug of some sort.

If it looks like your volume is intact using diskutil, you might want to restart the system, and immediately hold down the alt key and keep holding it down. A list of bootable volumes should show up and with luck you should then be able to select it and boot from it. Be careful though trying to copy some stuff to the Yosemite volume because like I said the preceding paragraph, it may not work.