Bootloaders and Pinouts

Attempting to bootload a atmega1284 (44pin tqfp). I am using mighty-1284p/boards.txt at v1.0.6 · JChristensen/mighty-1284p · GitHub and checked the fuses with the datasheet and everything looks like it should work. Pretty sure I bricked one already and being very careful not to brick another. The only differences I see are the signatures and the pinouts.

atmega1284P - 0x1e 0x97 0x05
atmega1284 - 0x1e 0x97 0x06

Changed the signature and bootloader fails and chip is bricked. (checking the signature with another arduino but fails to see it after bootloading)

The only problem I can see now is the pinouts (they are different) but not sure how a bootloader adds the pins_arduino.h file and if it is just the pinouts wouldnt the bootloader have worked but would fail to upload a sketch?

Always triple check your schematics.. wired it wrong, it works

If "burn bootloader" results in the chip no longer working over ISP programming, you're setting the fuses to use an external clock source (or setting them to do something else they shouldn't), but no clock source is present - likely it's set to use an external crystal, but you haven't connected one.

Also - you do have the bypass caps (0.1uf between ground and each VCC pin right next to the chip)? If you don't, programming can fail (with unpredictable results)