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NSX chassis

91-94 all have the exact same chassis regardless of transmission. 95-96 Targas have a reinforced chassis through the B pillars and side sills using thicker aluminum extrusions. Again regardless of trans. 97-05 have the same reinforced chassis as the 95-96 Targas, regardless of trans and regardless of coupe or Targa. They also use lighter body panels compared to the 91-96 cars.

Your tech is wrong. I fully swapped my 92 to MT including the cams and valve springs. Changing the ECU is as simple as cutting a single resistor and boom you have a MT. Unless you change the valvetrain I recommend keeping the AT ECU setting.
Regarding to ECU R04 resistor removal, will it also increase the max rpm to MT engine level!?