Engine swap now clutch doesn't fit right on crank
 

I have a 06 Dodge Mega Cab that I swapped out motors. I thought I had another 06 but apparently I screwed over with an older model block. Anyway I am moving over my stock clutch setup from the 06 to the 04. Seems the center hole in crankshaft is slightly smaller and my 06 dmf will not seat properly or bolt to flex plate truly. Does the Dmf have to bolt to flex plate a certain way? Or what should I do? What flywheel do I need to buy and will it be ok size like with my 6spd? Money is very hard to come by so I can't afford Valair or Southbend clutches.... Advice please. Is it possible the new motor came from a automatic reason it doesn't want to interchange with my 06 clutch? Help please.

Should be no difference!? You say flex plate? That needs to be removed to install a Flywheel!?
Post some pictures! You start with a clean crank shaft then bolt the flywheel to that MUST use manual flywheel bolts! DO NOT use the automatic flex plate or bolts!
I would seriously beg borrow to replace the DMF! BUT if it's still good and funds are tight guess it's good practice!
Bolt up the clutch loosely and use alignment tool to line up the disc with the pilot bearing....which should be replaced or at least lubed. Then tighten down the clutch to the flywheel be sure the tool pulls out easily if not loosen it up again and adjust.
You got guts for doing the job yourself and brains for asking for help! SO good luck and ask away!:tu:

I recall a buddy of mine had a problem with a clutch on an 05, and there was a different crank between a manual and auto in the early 05 and and late 04. the details are a bit foggy, that was 7 or 8 years ago.