not sure but happy to float some ideas:
heat expands things, you may have a joint/2 traces that cause a short when they expand but don't touch when they are cold. do a visual on all traces and 'new' work looking for stuff that it close together. this will help you rule out wiring/traces.
test 'easy' components with multi meter looking for shorts - resistors (ohm tests), diodes (diode test) and caps (cap test if you have it or continuity).
does it die at 'exactly' the same point after boot up? - could give you a clue if it fails when a certain component is activated.
replace all connectors.
if you have eliminated traces, connectors and the simpler components then start with the IC's. start where it gets hot and start replacing IC's one at a time until you find the culprit. (use sockets)
if at the end of this process, you still can't find it, then throw it away as its probably posessed!
the other thing you could do is have it bench tested....might get to the root of the problem faster..
all the best
