Peter,
At least one problem is with the silencing circuit, with R28. If that pin isn’t high (around 5v) then the output will be silenced. Please make sure the isp header pins aren’t shorted. Also make sure C18 isn’t shorted. See if you are getting 5V on one of the pins of R29, as the schematic indicates. If there are no shorts across any of those pins (checked with a multimeter continuity tester) then temporarily remove C17 to see if the shorting circuit is broken (heat up both pins at the same time while gently lifting it off; then use a solder sucker to clean out the holes). It is possible that the FET could have been damaged.
Don’t worry about the voltage discrepancy on the U2 pin for now.
Unfortunately, we’ve packed up all these circuit boards into kits, so we don’t have any available to sell by themselves. The good news is that circuit boards are very difficult to damage past the point of repair. If traces are broken, you can always run jumper wires in their place. If pads are lifted, you can always run components point to point or connect them with wires. There’s almost always a way to fix circuit boards…the schematic makes it pretty easy to see where everything goes.
Let me know what you find.
-Brach