I could be wrong but I think the tranny will fit. The 00GT clutch will not fit the 03GT engine. The 00GT engine has a 8 bolt crank/flywheel and the 03GT engine has a 6 bolt crank/flywheel. Doesn't matter that the 03GT came with a 11" clutch because I used a 11" clutch (FRPP cobra upgrade clutch, 8 bolt) in my T45 00GT. Get a new flywheel.
Like I said, I could be wrong, but I don't think so. You need a 6 bolt flywheel, that is a given. You have to make sure the new flywheel will be able to bolt the old clutch on. If I remember correctly, some flywheels can take both 10.5 and 11 clutches while some might not.