Assumimg that your hardware mix from different sources has not assembled incompatible (in ROM/firmware terms) bedfellows, only one potential fly in the ointment strikes me. You have already hinted at it. The PMU. The PMU is a 'puter-within-a-'puter, and has a 'mind' of its own. When it is reset you must be careful not to let the switch 'bounce', because the second contact can undo the good work of the first. A single push of 1-2sec is needed for reset. One sign that the first attempt has gone agley will be that your nice plump PRAM battery has declined from 3.6V-odd to zilch in a matter of days.

If this is the case, try resetting the MLB by removing all power sources with the mains cable still attached to the switched-off wall power socket to provide a reliable ground, and then lastly remove the cable. Allow half an hour unpowered and unconnected, and then start again from the ground up, with a spanking new 3.67V PRAM battery, keeping the old paws well away from the PMU area, yourself well grounded as you work, and with that unpowered power cable well connected. Insert the PRAM battery just before you reset the PMU, and then close the patient up promptly. Cross fingers.

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