Digest & ligate isn't even the worst problem. Back in the day (2006) the quality control and standardization of bricks was dreadful, I haven't seen evidence that it's improved substantially since then. Polymerases per second (POPs), the measure of brick efficiency, seems like a bit of a pipe dream -- I'm yet to be convinced that it can survive brick composition.

Did you do iGEM? Back in the day I started the iGEM team at Brown. We couldn't scum a PCR machine off anyone so we spent the summer doing minipreps. A few weeks before the jamboree, we refined our models a bit and showed that the parameter space in which our project would function was so narrow that it would probably never work. Oops!