Sounds like they may have under quoted you labor hours. Usually due to: Lack of experience, lowballing to hook you in for more labor, lack of skill, poor management or combinations there of.

A well run shop would have your engine/trans and front end sitting on a K-member waiting for the car to come out of paint. One experianced person in a outfitted shop could make it a roller in 16 hours...That is unless the owner is holding up the process with parts.