I haven't figured out the tranny sitution yet, but looks like its going to stay auto
as it is probably a lot of work to change the car from Auto to Standard.
Are you facing a time constraint of any kind? Just curious, 'cause I find it a bit odd that although you've comitted yourself to an engine transplant that you appear concerned about the amount of "work" to transplant the hydraulics from a stick car in to yours.
Ask yourself this: if I really don't like automatics, do I want to have to pull the drivetrain a second time to convert to stick at a later date?
On a lighter note though, if you had purchased "your baby" back you'd have a ready-to-go stick setup, complete with a 5 speed instead of the tractor-geared Muncie it came with.