You need the dowels on the flywheel, but you also need the dowels that are in the back of the block that align the bellhousing-which are most likely there. They are what aligns the tranny with the block. As far as the crankshaft/input shaft misalignment, that usually happens after someone align hones a block, and the crank moves upward.
The alignment tool you're describing is for aligning the clutch disk while tightening down the pressure plate, so its centered with the pilot bearing. The input shaft is straight(obviously) so if your clutch and pilot bearing are off centered, your going to have a heck of a time trying to get that tranny in there.
The alignment dowels on the flywheel are for centering the pressure plate. There is too much free space in the bolt holes, so it would be very easy to get the pressure plate off centered. Even a few thousandths offset could cause some vibrations. If you really didnt use the flywheel dowels, I would look into that.
The alignment tool you're describing is for aligning the clutch disk while tightening down the pressure plate, so its centered with the pilot bearing. The input shaft is straight(obviously) so if your clutch and pilot bearing are off centered, your going to have a heck of a time trying to get that tranny in there.
The alignment dowels on the flywheel are for centering the pressure plate. There is too much free space in the bolt holes, so it would be very easy to get the pressure plate off centered. Even a few thousandths offset could cause some vibrations. If you really didnt use the flywheel dowels, I would look into that.