The error you report in your second message seems inconsistent with your receiving any mp3 files at all in your uploads folder. If the Ajax post fails, then it never reaches your server, so however you got that error to show up, it’s probably not why you got blank mp3 files.
What browser are you using? Safari (especially the iOS version, but some desktop versions too) is known to have bad to no support of audio capture.
When you ask how you can combine the regular ibex trials with the PennController trials, what do you mean exactly? Judging from your code, it looks like it’s already what you are doing.
NB: you should use .log() before .record() to make it easier to pair the files your receive on your server with the lines in your results file.
NB bis: I edited the code in your first message to replace the URL to your php script—attacks are unlikely but it’s always safer not to expose a public way of uploading content to your servers