Model looks fun, and I think it's gonna be ok! 

I know this is simple, but take off those big chunks of glue with a hobby knife, use a clean #11 blade and it won't be too hard to get through.

Looking at the primer issue, I'm wondering, did you clean the parts well before painting?  If you haven't heard the deal with the release agent they use in molds, and how it's used to get the parts out, but still remains on the parts afterwards, well, now you know!  lol  Most people use an item you can find anywhere called "Simple Green", household cleaner.  Must be diluted, cleans parts wonderfully, and is phase 1 of making sure any paint goes on well.  Also, did you use a rattle can or an airbrush?  If airbrush, working with your pressure can help paint problems too.  With rattle cans I think you gotta go easy because you can really get too much in the first shot, you want a few nice thin coats.

Hope that helps a little, I have the beginnings of one build up at modelnoob.com, that may have some good hints for ya, and show you how working with three types of putty and epoxy all panned out.  The best deal with that is try them all.  They all behave a little different, and over time, you will know what to use where. 

Good luck, can't wait to see the final!

Joe