I've 301'd the pages I want to go to other pages on my new site from my old domain.
That's about 25 pages of a 100 page website. Each page goes to the new location on my new site. Is there a way to redirect all the rest of the pages, say to the new site home page, or do I need to set up rules for each page?
Also, some of the pages have different file names on the new server but virtually identical content. Will this affect the Google juice I'm trying to transfer or is the best way to keep the file names identical (which I cannot do)?
Yes, there certainly are ways to do what you want, but the technical details for redirects are something better discussed in the forum for specfic server that you are hosted on - Apache [webmasterworld.com] or Microsoft IIS [webmasterworld.com] most likely.
...some of the pages have different file names on the new server but virtually identical content. Will this affect the Google juice I'm trying to transfer
Not to my knowledge - the target file name for a redirect should not make any difference. However, as you may well know, when changing to a new domain it can be take quite a while to see the effects kick in.