Beau--what a disaster! You have my sympathy! I'd be ready to "key *his* flute..."
Regarding my thumbs--they stopped hurting after about 4 days of playing about 20 minutes day. Now if I play more than 40 minutes, they get sore, but only for a little while. I think I have bony thumbs.
The up-side is, I love this instrument. I've had two lessons, and I'm having so much fun! I don't mean to brag, but I've learned about 10 simple songs (e.g. Twinkle Twinkle) and can play them fairly cleanly. Whole notes are tough because I seem to run out of air, and 1/8th notes are difficult because I'm not quick enough yet, but I'm working on it. I need to soften my attack, to get rid of an initial "puff" sound, but (unlike with my guitar at this phase) I can see little improvements every time I play. SOOOO Rewarding!!!!