No you can boot the board without the header pins.

try a manual reset. force cpu p40 low for a moment. Easiest way to do it on a 6800 cpu is just use a flat blade or whatever and bridge p39 and p40 together for a moment.

Switcher supplies power rails do not come up in the some way the original linear supply does so the CPU may not reset properly.

All you need is +5V to TP5 and GND to TP4 and +12V to TP2. This should get you to 6 flashes. To get the 7th flash, short TP3 to TP2.

Instead of shorting CPU pins 39/40, you can simply pull the +12V off of TP2 for a moment to trigger another reset.

For the 7th flash I jumper the top of R17 to the top of R23. Probably the same result but the test points do get crowded

Then, assuming you have good phase 1 and 2 clock signals, it sounds like the CPU cannot access the EPROMs to start running the program.

This is where we usually ask for close up (in focus) photos of the area from the 6810 downward.

Of course, one check for you is to do continuity checks for DO-7 and any of the low Address lines from the 6800 to the 6810. This checks a number of lines that are in the "problem" area.

Of course, most of us that do a lot of these boards usually replace sockets for U9 and U10 as well as U2 and U6 before bothering to play with it further. That's assuming, you can unsolder a socket without doing more damage than what you started with (no jab at you or your skill set, just a reality of many home brew techs out there).

We need FOCUSED, WELL LIT pictures, front and back.

Did the board ever work (or did you buy it busted?)?

Is is jumpered for the correct ROMs?

Is the memory chip good?

What are you using for a bench supply?

P21 to 40 can be traced back to the other PIA. There is just one address pin different I believe.