1284p Bootloader w/Arduino as ISP

Try connecting your ISP programmer again and doing another Tools > Burn Bootloader as a test. The first time you did it the microcontroller was likely running on the internal clock, as that is the factory default setting. But when you did the first Burn Bootloader, if you had Tools > Clock set to 16 MHz external oscillator then it changed the fuses to use the external clock source. If your crystal isn't working this will cause the second attempt at Burn Bootloader to fail since the microcontroller now requires an external clock source to run.