You can upload a custom php.ini file to your /public_html/ directory and then use the steps from our guide on how do I make my php.ini file recursive in order to use those settings for your entire site.
Otherwise your account will just use the server-wide defaults in the main php.ini file that your user doesn't have access to. I went ahead and made a copy of the server's default php.ini file and left it in your /public_html/ directory if you wanted to modify any of the settings.
Currently your PHP post_max_size setting is set at 128M so it shouldn't be this limitation that is causing your upload cut off problems. Your max_input_time is also set to 60 which should be allowing enough time for sure to upload more than 5K worth of data, same with max_execution_time being set to 30.
I used a quick PHP upload script and confirmed I could upload an 11K text file without issues. I left this test up for you at /Development/test if you'd like to look through it.
I took a look at your /Development/file.php script which seems to be where the POST data is getting sent to, one thing I noticed is that you have a line mentioning this:
if (file_exists("upload/" . $_FILES["file"]["name"]))
However there is no /upload/ directory anywhere on your account. When you're uploading files below 5K in size are they successfully being uploaded to the server at all currently?
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