[ozrien]

You can use PWM to control Jags, that's legal. Which rule did you read that made you think otherwise?

To keep things simple, I would try to reflash each Jag one at a time using BDC-COMM (just like you described) using serial only. So in other words...
Laptop/PC------ UsbToSerial adapter----------- serial rx and tx on RJ11 on the left side (See Jag doc for pinout).

That should work for discovering one jag and flashing it with BDC-COMM. No need for termination resistor or rj11 daisy chaining since your just using BDC-COMM to reflash.