Assuming it's not the ABS module (I've never heard of anyone having to bleed the ABS unit on a car, but I'm no expert), it sounds like air somewhere. But you seem to have enough mechanical aptitude to bleed brakes properly, so that's probably not it.
The only other thing I can think of is that maybe a piston seal in the MC was damaged when the system was empty.
The FSM usually has diagnostic procedures for troubleshooting. But they often require the use of Nissan's software (I forget what it's called). Worth taking another look.
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