Bart,
It has been a while since I've gotten a close look at a Commander II vibraphone. Even if you can remove the damaged rail from the frame and replace it with a new cut of wood, replacing all of those pegs is going to be a major pain in the behind (get your drill press warmed up!).
FWIW, I refinished the frame of my ProVibe a few years ago, and I removed the rails from the end panels in the process - cracking one of the rails, but it was one of the inner ones adjacent to the damper bar, so the cosmetic significance is minimal. It was a matter of me removing the screws connecting the rail from the end panel, and then knocking it loose with a mallet (woodworking mallet, obviously, not a vibes mallet!) - whatever glue they used didn't put up that much resistance. Perhaps the same thing is possible with the Deagan? If you can do that, then 1) cutting a piece of wood to fit won't be that difficult, and 2) you can buy the pegs from Century mallet, I'm sure.
Have you contacted
Gilberto Serna about this? ( 773.248.7733 ) I'm sure you know already, Bart, of Gilberto's association with the Deagan company, and the fact that his
Century Mallet company is in the old Deagan factory in Chicago. At most, I suspect you'd only need to ship the frame to Gilberto, since I'm sure he has the original spec's for the instrument on file. If the rail can be removed from the frame, perhaps he could just make you a new rail, and ship it to you, leaving the installation to you in the process?
Another option would be Brian Stotz'
Repaircussion shop up on Rochester. I don't have the number handy, but I'm sure you can find an ad for him in
Percussive Notes. I've not made use of Brian's services myself, but his reputation for doing good quality work is outstanding.
I'd call Gilberto before Brian, ONLY because you're dealing specifically with a Deagan instrument - go to the country's top expert, and if he can't help you, contact Brian.
I'd take another stab at posting to thevibe.net - there are a number of Deagan owners who are regulars on the board, and maybe one of them could offer their perspective - as much as I'd like to have an old Deagan in my arsenal, it doesn't seem to be in the cards for me at the moment...
If you can't find Brian's
Repaircussions number anywhere, let me know - I'll see if I can dig it out of my files here. And if you need any help dope-slapping that "helpful" stage-hand, I'll look into flights from Hartford to Dallas...

... you don't do that to
anyone's instrument, but ESPECIALLY an old Deagan!!