I can see where this project is going, and hope that you are successful in making this program a success. There aren't many MIDI / ORG converters out there (if any), and this would greatly help the CS modding community.

....And now for the criticism.

Honestly,
not many people use MIDI files. I couldn't even find an MIDI file anywhere on my PC to test this with. And most of the MP3/WAV to MIDI converters I've seen are crap. This fact alone is a pretty big problem.
....And there's a few errors.

I found a site that has a huge collection of MIDI files. I downloaded a song from there (I_Gotta_Feeling by Black Eyed Peas) to test this out.
Site:
Song:
(The song is renamed to feeling.mid)
I placed the file into the same folder as the program and ran it. Entered song name (with .mid on end). Crashed (at the same point as the image below).
I closed the program, deleted the two (.dat) files it had created and instead made a (.dat) version of the song using the
Midi2Text.jar included in the file. I placed it next to the song and re-ran the program. The image below is what happened.
The program crashes at the exact same point as before. However, after clicking "Don't Send", the program continues to run. The image below shows what happens.
In the end, no ORG file is created.
Ya' might want to fix that.
...That's about it.
Imagine a gigantic cyborg, vaporizing people with one hand and spewing Plasma bolts with the other, and at any moment it may go crazy and target everyone as enemies.
Sometimes, I'm glad I'm not a Komato.