Aperture is trying to upload my entire 15,000 photo library

why is iCloud tring to upload my entire 16,000 photo library to the cloud when it will only hold 1000 pictures?

It's not an Apple problem but a computer problem in general.  One reason could be a bad block on the external HD.  Another could be a damaged image file that was able to be imported to the library but can't be read fully for copying.
You can try using paid version of  iPhoto Library Manager to rebuild the library and have it put the rebuilt version of the EHD.
Using iPhoto Library Manager  to Rebuild Your iPhoto Library
Download iPhoto Library Manager and launch.
Click on the Add Library button,                         
and select the library you want to add from those in the selection window.
Now that the library is listed in the left hand pane of iPLM, click on your library and go to the Library ➙ Rebuild Library menu option
In the next  window name the new library and select the location you want it to be placed.
Click on the Create button.
Note 1: This creates a new library based on the LIbraryData.xml file in the library and will recover Events, Albums, keywords, titles and comments. However, books, calendars, cards and slideshows will be lost.
Note 2:  Your current library will be left untouched for further attempts at a fix if so desired.
OT

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