I'm currently working in OS X 10.10.3. I made a bit of a jump from 10.6.9 as our system was falling behind from the person who previously held my position. All of my customer files are stored on an external HD and up until my Yosemite update, indexing has worked fine. I've reviewed several other posts and gone into Terminal and disabled/reenabled all volumes to index and still nothing. It is getting very difficult to find files that I didn't file when I cannot search my drive!
Old school way of trying to solve it but can you get a second HD? Format that using Yosemite with Mac OS Extended (Journaled) and copy the files over to the new drive. The new format might make it be recognized and indexed by Finder at that point.