Photos/iCloud syncing issues...

I am wondering if someone can tell me if this is to be expected or "normal" behavior. I have a large photo/video collection (e.g. 45,000 total with roughly 1,500 being videos). Newer photos and videos are larger files from iPhone 6 and also photos from a Nikon D7000. I upgraded to Yosemite and purchased enough iCloud storage to more than cover my current needs (I was just under 100 Gb and have the 500 Gb plan). Uploading all of my media to the iCloud took weeks. I set my iMac to never sleep and after a few false starts (couldn't believe it was taking this long so rebuild the Photos library) I let it run. Like I said, after weeks of running my media collection is available in iCloud/Photos. I also have local backups on a TimeCapsule. Once the initial upload happened my images starting syncing and the iMac was speedy once again. Then my hard drive died...

I replaced the hard drive, restored from my TimeCapsule backup and was off and running until I fired up Photos on my iMac. All my media was there but then it started to go through the routine of "preparing media". This only took an hour and I was expecting it to do this preparation and then reach out to the Photos in iCloud, discover that they are all there and be done. Well, it determined that it needed to upload 33,000 of my 45,000'ish media items. I let it run overnight and the number didn't change (e.g. didn't upload anything or decide things were OK). Out of frustration I rebuilt the Photo's library on my iMac, it did the check again and determined it still needed to upload 33k media items to the iCloud/Photo.

When I originally was uploading my media collection, it would seem to get stuck and I would plug my iPhone in and have it upload a picture. This seems to kick off the process again of uploading to the iCloud. I tried that this morning but it was taking way too long and ran out of time before it completed. Oh, I have restarted the iMac at some point (after shutting down Photos) to make sure the iMac wasn't in a weird state.

Any help or guidance would be great. I'm not sure if I should just wait days on end to see movement or if I have a real issue. It is unfortunate that iCloud/Photos didn't recognize that all the media is already there.