I'll try to answer some of these as best I can, but I've not built this model. However I do have the old version from the Adversary kit in my stash, it's one of the first kits I want to build once I'm able to do it justic. I love this ship!
--What size of drill bit do I need for the windows?
Have a look at some reference pics for accuracy. I always use a google image search, however the studio model can be seen in some nice detail here :-
http://www.modelermagic.com/?p=9506
Drill bits below 0.5mm are very brittle and will be hard to use. However on this scale it would be necessary for accuracy. I don't think anyone could blame you for going larger than 0.5mm, though I would have some spares at hand in case the bit breaks.
--What brand/color of spray paint do I need for the primer?
I'm still very inexperienced to give advice on primers and paint tips. Tamiya is the best I've used and comes in grey and white (I think that's all there is). I don't think it matters which one you use for this model.
--What is the brand of red putty I've seen most of you use to fill gaps and seams?
I think that's Bondo spot glazing putty. Read Grendels Desslok's Command Cruiser build. He tries some different seam filling methods and this is one he tests.
--What colors would work best for the lighter and darker shades of green for the final paint job?
Again, a more experienced modeler could help more here. I'd say it comes down to your preference though. Do you prefer acrylics or enamels?
Also, there are different colour schemes for this ship. The early ones were very bright green, whereas the Warbirds seen in later series and DS9 were darker and had more detail painted in (I believe those were the CGI models).
I'd have fun with it myself. Try and find a mix of greens that you find suitable.
--What kind of glue/epoxy do most of you use for your models?
Personally, I've grown fond of Zap CA glues. They have different consitencies that you can get. The medium one is quite good for general use. I also like Slater's Mek-Pak styrene cement.
Epoxy resin? I use whatever is available in my local shops. 2 part epoxy resin is handy stuff, I prefer a 15 minute for most situations. 5 min doesn't give you much time, and 1 hour is too long for alot of stuff, it runs everywhere.
Apoxie is different. It's a putty. I've used Magic Sculp (no 't') in the past, and it doesn't really hold, but is useful for sculpting, supporting and strengthening models. Also useful for fixing LEDs, but don't use too much, because your model will become very heavy! I also use Miliput.
However, I've recently got my hands on some Aves, not readily available here in the UK, but it's by far the best and can be used for seam filling very effectively as well as sculpting. It's really awesome stuff.
Hope some of that helps.
