We use Docutils reStructuredText (a LaTex frontend); that gives you your .txt source. Then I wrote a Python tool to create all of the HTML/PDF formats you're looking for, including the 3-frame SDK-style HTML documentation with table-of-contents, index and search capabilities. I read an XML file that specifies the source to be included in the document. It's all very automated and runs as part of the build.
It works and you'll probably like it but I don't recommend that approach. Documentation is best completely separated from software development unless it is fully integrated into your software development methodology, which is quite rare these days (the foremost and obvious reason being that most developers don't write). But if your project is small enough and you have complete control over all of it, the way we do it will work for you also. The number of pages has little to do with complexity and you probably won't run into scaling issues for a long time, if ever. The number of dependencies between pages is a much more important parameter, which will become nearly unmanageable after only about seven pages.