What did you use for a floor shifter, OEM or aftermarket?
Does the transmission have external shift arms? Lets assume it does.

Hurst has detailed instructions on how to set-up their shifters / linkage. I had a '70 Nova with a Hurst "Indy" 3 speed floor shifter. It would periodically "hang" when shifting. I re-adjusted it per the Hurst instructions and the problem went away.
Hope that helps.
John