4spd swap checklist for a 68 Dart GT 318/904

Maybe it was mentioned but I did not see it,,,, and having the motor out will make this easier, dial in the bell housing with the bell mounted and torqued to the block.
Manual transmissions are much more sensitive to alignment than automatic transmission are.
There are several sources for offset dowel pins if needed.
RobbMc has good ones.
And just because a crank bore is drilled to depth that does not mean it is honed to size for diameter. Ask me how I know that.
With a crank that did not have a bushing in the crank bore I will always carefully measure the diameter prior to pressing a new bushing in.