if hes got a 91 turbo harness in the car he can use the 5spd with the 5spd ecu out of the 89 with the 91 auto harness and the 5spd tranny and all will work fine..
when I had my black 89 turbo 5spd supra it was an n/a I used a 7mgte with 5spd 7mgte ecu from a 90 supra and a turbo auto engine harness and everything worked great.... just had a few extra connectors not needed....
the sensors are the same on the engine from 89-92 7mgte's only difference in the engine harness is the body connector that connects the engine harness to the body harness.. ecu's are the same...
and since he stated he wanted to stay 5spd then I would. Its really not any harder then keeping the auto and no reason to not drop the 5spd in the 91 if he wants a 5spd.. since he has everything needed to do a 5spd swap( tranny, ecu, pedals, clutch master cyl, slave cyl and all the clutch lines....) it would be crazy to keep the auto in if he wants a 5spd... and a 5spd tranny with 5spd ecu and auto trans works fine no issues at all....