I am watching this thread with great interest, as I have had my own struggles with coating 'film'.
IIRC, strong solutions of acetone (and most ketones) usually soften PVC. Perhaps there is some plasticizer or other additive in the product. I don't know if it's the case with Clear-Lay, but I've found that many plastics and papers benefit from a wash with water + surfactant to remove manufacturing residues (lubricants, powders etc., used to facilitate machine production, packaging), sometime a good puff of compressed air is enough.
I'm currently using fixed-out imagesetter film as a base material: it is very clear, dimensionally stable, and the subbing/emulsion layer is very tough.
Looking forward to hearing more about your adventures!