So I've spent the last few days trying to troubleshoot my Nava build. The build took me around 3-4 days and was straight forward. Unfortunately on power up I'm getting odd behaviour and the unit isn't functional.
The main issue is with the display - I get top row all blocks and the LEDs across the board exhibit random behaviour upon each power up, inconsistent. I first replaced IC115 (EEPROM) but still had the same behaviour. I then traced top and bottom layouts of just the sequencer section and removed all other ICs in all instruments and only left ICs in the sequencer section. Still the same behaviour. I then tried to remove everything else and leave just the Atmega1284p and used my Arduino Uno to try and see if the chip was OK.
At this point I could not read or get any useful info from the chip or even reburn the boot loader. So I decided to try and factor out the PCB and I built a breadboard to see if I could read the chip from that instead. Success, I could read and refresh the Atmega chip! I popped it back into the Nava but the same symptoms were shown.

I've checked continuity between the main pins on the Atmega and the ICSP header and all are there. Remember, all other IC's are not populated so I'm effectively using the Nava as a breadboard, but I cannot read the Atmega from the Nava board.
I'm at a total loss here, the circuit I built on the breadboard is simple - pin 6, 7, 8, 9 for MOSI (also with 10k to +ve rail), MISO, SCK and RST, pin 10 and 11 +5V and GND. Pin 12 and 13 with the 16Mhz crystal and 22pf caps to ground off each. On the analog side, 0.1uF cap across the +ve and -ve rails, that's it.
Can anyone suggest what I can look at next? All voltages across the board are normal at all the relevant power pins on all ICs. When I had all components populated, I couldn't get into TM2 calibration, nor get any voltage from TP1. I've also tried initialising EEPROM (blindly without display) but this also didn't seem to work.
The issue with my unit seems to be that the Atmega is not functioning properly while plugged into the board. Any help much appreciated! I'd still like to try troubleshoot more with some guidance as to where to look but I may resort to paying someone for repair. Any takers?