Keeping the 2.9 and working the motor is your best option... you made your bed, now lie in it.
I don’t see the M5OD being very happy at 6500 rpm, but you’ll have to find that out on your own.
The 13-54 is a good T-case, stick with it. I’d pull it apart and check the condition of the oil pump and chain. The only issue they have is the tab on the pump wearing and allowing it to spin free.
Explorer 8.8 and D35... ??
A spool is a solid locked rear... you don’t want it for the street. Torsen, Detroit, air locker, E-locker... Take your pick.
Don’t worry about redline for your gear ratio, worry about your torque. If your torque is low and comes on slowly, 4.11s. If your torque is high and stays steady until redline, stay with 3.73s.