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I've never done a troll either. But I've done 2 falcons. I got all the factory manual bits.
Gear box
Flywheel / clutch
Drive shaft
Clutch pedal
Interior trim / center console
Ecu.
Put it in and no problems. The tunnel holes match up and gear box mounts are there. Hardest part was putting the cluch pedal in. Which wasn't hard BTW.
I'm pretty sure the man and auto in the gqs are the same length though so shafts shouldn't be an issue. Also it should bolt in the same holes as the auto. Cos they come out man and auto it would be stupid if they had to make 2 diff frames and body's just to put a different box in. Start by confirming you have the holes for the clutch booster in your firewall that'll show how easy the swap will be.