I also know what you mean on drilling holes in the body - back in the day I had full length ding protectors on my cuda that were drilled and riveted on! So when I get started on body work I think I have about 20 drill holes to fill in, but from looking at all the major metal work that guys on FABO regularly do, these should be an easy but probably pricey fix.
Bummer on the window, that crack fix looks interesting and maybe worth a try if not too pricey.