I was the Vacuform Operator at MLRC, and despite every trick we could think of, it was very challenging to get a clean pull.
The bucks is that they need to be glass-smooth, otherwise a good repro will also pick up any printing texture.
Problem is, the polishing of the buck creates a static charge that is hard to dissipate, there is also static in the sheet clear. and just one or two little nits will stand out. Maybe try some dryer sheets?
If the molded parts pick up contamination, the solution is to surface and dip the clear, FSM has had a few articles on how to micropolish scale aircraft canopies to deal with this.