Thanks for the responses!
I did a little checking on the throttle linkage. Dad said he set the linkage and accelerator pedal height per the shop manual with the 1/4" drill bit to lock the pieces in place and get everything set. I have not double-checked his work, but it looks correct. What seems to be an issue here is the throttle stops at about 1/2 travel. If you remove the kick-down rod it moves completely open with no resistance. I can't believe this was not noticed until now. I've included a link below to a video I made to help explain what I'm looking at.
https://youtu.be/_61b9NP3g2Y
This was an issue when we put the transmission back in and was explored then. I thought this had been resolved but obviously not. For the sake of comparison, I made a video of a friend's '57 thunderbird with the same functioning setup and his kick-down rod appears to have the same amount of travel (approx. 1")
https://youtu.be/W6HoDwVATnk
I'm going to go back through the steps listed in the manual on setting up the bell-crank linkage and see if that possibly changes things. If not, maybe something is possibly bent or needs to be looked at closer.
Would any of this indicate a stuck throttle valve as Dominic Hide suggests? I feel a positive stop when depressing the rod and it springs back up to the top again. Possibly a bent bracket on the throttle body that bbrocksr mentioned?