I still don't think it's possible to pull the input shaft out of the clutch
or torque converter with the tranny installed. You don't nearly have enough
room to move the engine to the left. There's barely enough room for a
timing belt change.

Civics of that era had different engine controls. For example, automatics
had EGR and manuals did not, which means the heads are different, as are
the ECUs. If you wanted to put an engine from an auto into a manual, you'd
have to transfer the ECU, all the EGR hardware and wiring, and lots of
other stuff to make sure the Check Engine light would stay quiet. Or else
you'd have to know exactly what you were doing in order to make the
existing ECU think the engine was the same.

This is a big project. And if your state has an emissions inspection, you
will need to be certain you've transferred everything over that needed to
be, otherwise you'll fail.

It would be far, far better for you to locate an automatic Civic from which
to rob the engine.