Did you say that the slow boot problem that you were having was a
machine with ISA?
Would it make sense to put in a POST card, and make a new [temporary] BIOS
with its POST peppered with OUTs? Just seeing any output that would let
you know WHERE in the process it was getting bogged down might help.
It could be as trivial as it trying to access hardware that isn't there,
and not moving on until it gets a timeout error.