instead of JDownloader reassembling all of the .rar files I have an .iso file as well as 300+ .rar files in the folder that I designated the downloads to go to.
This sounds like exactly what you should have ended up with (the RARs should have contained the ISO file, so the ISO file is what JDownloader extracted from the RARs when the last one finished downloading), so I don’t know what the problem is. Did you have problems burning/mounting the ISO? Or were you expecting an MKV or similar video file and just assumed an ISO disc image file wasn’t right?