Wow!
That seems pretty impossible to me. I cannot see an automated way to merge (mixing) paragraphs from two different html files into a single one but by copy/paste-ing each one of them in the desired place (and as you say that's pretty time consuming)...
The rest of the troubles (links with the same id) are possibly more or less easy to solve.
But nevertheless, I would like you to ask you what your html/css/epub knowledge is. I mean, mixing two books is not only mixing the text. You have to watch how the styling of each book goes (CSS) and how you need to port them. Or, as you have suffered, if you have links (I suppose through <a> tags) you have to correctly re-link them. Also, you are talking about a Russian book so *maybe* it also has embedded fonts as not all device default fonts have enough unicode support and therefore adding a good font to your book is probably a good idea...
So there's a lot of small (and not so small) issues which can arise in the process. Unless you do know at least some basic html/css/epub coding, I don't see how you are going to success...