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Yeah I think all NBs with 6-speeds had 3.909 torsens except the MSM.
Pretty sure you're right- I sourced my Fuji 3.90 LSD from an '05 non-MSM. Combined with the '04 MSM motor and six speed it should give the car good legs.
Speaking of diffs; I have the open '99 rear that came out of my car if the OP needs it. (Or anybody else.)