Actually, as you've already got both on hand it'll be plenty evident when you start swapping parts. If you're keeping the A/T ECU you'll want to route the neutral start switch through the clutch switch. Then you'll need to swap transmission, clutch master cylinder and lines, brake and clutch pedals, clutch switches (one acts as the NSW and the other prevents the cruise control from over-revving the engine when the clutch is pressed), drive shaft.... there's more but it's just little things.
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