Probably a stupid question, but...Are the flywheels on the 4.6 specific to manual/automatic transmissions? Looking at Jeg's site, they don't specify, however they have a flywheel bolt kit says "manual transmissions only".
In a word, YES. A manual transmission uses a "Flywheel". An automatic transmission uses a "flexplate". A flywheel is heavier and has a flat machined surface for the clutch to apply to. A flexplate gives a way for the torque converter to attach to the engine. As the name implies, allows the torque converter to flex in relationship to the engine/transmission. In additon to the flexplate/flywheel question, there is also the number of crank bolts (6 or 8). AND certain model year cars have different size flexplates. For manual transmission, there are two clutch styles in use. 10.5" and 11". Size does matter. If looking to match an application, it is best to give the make/model/year/transmission as well as engine type and plant (Windsor 8 bolt crank or Romeo 6 bolt). There are even exceptions to the Windsor/Romeo thing (rare).
Manual transmission cars come with flywheels. Autos have a thin "flexplate" bolted to the crankshaft and the torque converter bolts to this. Both look a little bit alike but the flexplate is just a stamped-steel plate whereas the flywheel is heavier and thicker with a friction surface for the clutch disc machined into it. The center sections where each bolts to the crankshaft differ and have different fastener requirements. The flexplate requires a M10x1x20.5mm bolt (M-6379-A) while the flywheel requires a longer M10x1x26.5mm bolt (M-6379-B).
The reason I ask is that I'm wondering if I'll have to buy a manual trans. specific one for this motor I just picked up out of an auto equipped car. I unbolted the flywheel/flexplate (it's a 6 bolt) and wondered if this is interchangable for each type of trans. I'm calling it a flywheel as I've never fooled with auto trannys. It's what the starter teeth grab onto to turn the engine over.
Yes. You will need a flywheel to replace the flexplate. For a 10.5" clutch, get a flywheel from a 1996-1998 GT. For an 11" clutch, get a flywheel from a 2001-2004 GT. Try Car-Part.com--Used Auto Parts Market for salvage yard flywheels. Recommend resurfacing salvage flywheels before re-use. Ford racing parts for a new flywheel. The advantage of a new FW is they have dowel pins for both size clutches. As already mentioned, you will need new crank bolts as the ones you have will not work. A pilot bearing will be needed as well.