I'm with Graham on this one, Drill/file them out, then use some thing like Microscale Kristal klear or Gaitor glue (havnt tried it with gaitor my self).
I often use Kristal klear for windows in 1/72 scale boats etc.
Regarding the glue marks and finger prints; Have you tried useing a glass fiber pencil. I found it the best thing for clean ups. Takes the glue real easy and minimal damage, if any to the harder plastic.
Sounds real odd but if there are large blbs of glue, they can be softend up with liquid polly then removed more carfully afterwards.