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Quote from "Vlad R":

do not try to end the file with "?>"

I set some settings in customizables/config.php and I added ?> on the end. Every issue I had was fixed when I removed those 2 characters. Thank you.

I partly rewrote the Owncloud.cs file that is responsible for getting file uploading and sharing to work with Filerun. I updated the code to get the upload working, but I got stuck on the sharing part of the code. If anyone wants to take over where I left off, you can grab the work I've done attached below. Also linking the permalink to the original file so new commits can be  tracked and merged.
https://github.com/ShareX/ShareX/blob/f24a303d49f8fbff5c662d1343e2df7ee07cfd70/ShareX.UploadersLib/FileUploaders/OwnCloud.cs

Owncloud.cs (rewrite)