Ooooo that sucks.

I think trying to get the data off the bad drive would be the best solution. That way you would still have all the folders, edits and tags, etc preserved. However the clickng sound is not a good sign. It suggests it is more a mechanical hardware issue than poor data on the drive. Can the system even see the drive any more? If you can see the drive, I you could try running a disk recovery utility called Spinrite from GRC.COM. This is by far the best disk recovery utility available. I must have recovered data off of at least 20 drives at work over the years with this utility. You can download a trial copy and give it a shot. However, if it is a mechanical problem (which it sounds like it is), this utility will not work. This may seem crazy but I've heard that it does work the odd time. Put the drive in the freezer for a while and then give it a try (you won't have much time before the drive heats up again so you will have to be quick getting the data off of it). This is a last ditch effort when all else fails. Also how much is the data worth to you????? You can alway try one of those disk recovery companies where guys in bunny suits take your drive apart and put the platters in a new drive. This is not cheap. It may cost you $2000

As for Lightroom and your second drive. I know of no way you can easily get back all your folders. You could open the 11 month old catalogue. Lightroom will then indicate that it can't find the files. You can then tell it to search for the files in the one main folder that you have. You would have to repeat this for every folder in the old catalogue. This would at least preserve all edits, etc for those images over 11 month old. As for any files newer than 11 months, you would have to import them like they were newly taken and for those it would be like starting from scratch. i.e you would have no edits etc preserved. This unfortunately would result in everything being in one main folder. You woud then have to try to manually recreate the folders, and move the files (within lightroom) to the newly created folder. Hopefully the folder structure in the old catalogue and tagging you did would help you figure out how your folders were organised.

As for me I use a tool from Microsoft called SyncToy. I have to run it manually (and I do it after ever shoot i do). It copies files from chosen folders on disk A to disk B and preserves the folder structure. I'm sure there are other utilities that do this automatically but this is the one I use.

PM me if you would like clarification on what I have said.