If I open the MHT file with IE 11 it takes me to the interstitial ad page and if I block my internet connection in the firewall it just gets stuck at the interstitial ad. I guess somehow the interstitial ad redirect is still present even though I thought I had eliminated it by deleting the .js file. The interstitial ad doesn't display when browsing from the directories though.
I was exporting to MHT with all of the checkboxes unchecked. I've also tried exporting to MHT with various combinations of the options checked or unchecked and still no luck.
You could try CHM or EXE format for better offline viewing experience. Or we may setup other Projects to eliminate scripted links with URL Substitutes.