The New Photo App Not Syncing Properly

I've been pulling my hair out over the last week or so with the new Photo's in the iCloud and how the online database won't sync properly.
This is how I went about the upgrade.
I have a Mac Mini which has been for the past several years drawing down my family's photo's and video etc from all out devices using iPhoto. This has worked very nicely. I've been adding pictures from my stream into albums etc with about 200 or so. All files are stored locally of course in organized folder which is then back up on to a external drive.
After the latest update I opened the new Photo app and it started to convert my library over and started to upload all the photos, some 15000 pictures and a few hundred videos. I started to check my iPad and iPhone which is where I started to see problems, missing albums, missing photos, duplicates etc. Before anyone asks I emptied my trash in iPhoto before I updated as I had read about the new app pulling all the photos from trash in too.
After several days of stopping and starting my iPhone and iPad looked like it should with my albums and the correct amount of files. I checked the online iCloud Photos through my browser which also match, but I had all the old iPhoto months and daily libraries still showing despite me organizing my libraries not to group the photos in these old style albums.
At this point I also looked back on my Mac Mini to find that all the libraries had totally disappeared and there seemed to be a couple of thousand files missing, ie my ipad, iphone and online coun which is at something like 15,634 files and the Mac Mini Photo app was showing about 13,450. Plus, it was now saying uploading some 24,000 files but was in fact doing nothing.
At this point I decided to turn my main iMac on and see if I could get the databases to pull down from the iCloud to see if it matched. Three days later it's stuck at some 3200 files and saying it's still adding 15,000 files. I then went back on to my Mac Mini and started a fresh version of Photo and it's now stuck in the same state as the iMac saying it's adding file but nothing is changing.
Please help.

How did you import the photos?
Are the missing photos perhaps referenced? Then they cannot upload to iCloud.
You can check with a smart album, if you have any photos in the library, that cannot upload to iCloud.

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