For cleaning the glass from copper, Joseph Chikva proposes to use circuit board etching technique (of course without protecting any surface for the conductive path):
http://www.talk-polywell.org/bb/viewtopic.php?t=2126&postdays=0&postorder=asc&start=388

Here it’s described how you do it step by step (without Google translation):
http://www.wikihow.com/Etch-a-Circuit-Board

BTW, he also worries about hydrocarbon contamination induced by the Mylar insulators. I just want to mention this, so in case you get more unwanted hydrocarbons, these might be the source.