Hi,
1) As long as (all) UploadRecordings complete(s) before SendResults (eg. because you inserted UploadRecordings("upload") before SendResults() — no second argument in UploadRecordings, because otherwise it would be non-blocking and would therefore likely complete *after* SendResults) you will have a line for each uploaded zip file in your results file, which you can use to pair zip files with submissions. The recorded audio files are named after the MediaRecorder element that produced them. More details in this post
2) Unfortunately that is not currently supported, since all major browsers support only webm/opus when recording via the MediaRecorder API, which PennController uses in its own MediaRecorder element type. The webm files can easily be converted to wav files though, eg. using ffmpeg: ffmpeg -i "file.webm" -vn "file.wav"
Jeremy