I kept calculating the elapsed times from the 12 hour times, post conversion, and ended up with a ton of negative values! Ended up hugely streamlining the workflow while trying to figure out what I was doing wrong though, so not all bad!
I first padded the date to a standard format, then used the datetime tool on each date to convert to an alteryx format. I then calculated the difference using datetimediff() function and then converted the dates to 12 hour format using %I:mm and dropped the extra columns.