I've only read your GitHub's README, but the package seems pretty cohesive: tools for interactive modeling. It could definitely use a better name; I often search for new packages by using Ctrl + F on CRAN's package listing page.
The only odd feature I noticed was the APA ggplot theme. Maybe you could submit it as a pull request for the ggthemes package.
For your questions:
In some cases, definitely. With your package, I envision the same person using it for the same tasks (though at different points along the pipeline). But if only half a package applies to a user's work, that user shouldn't have to bother updating the package for the unused parts.
As you worried, "miscellaneous" packages often bloat and need divided. And sometimes, even with packages started with a clear goal, some of the underlying "workhorse" features would be nice in other packages. Splitting them off prevents copy-pasting code.
If you've been writing well-contained functions, it should be a breeze to create a new package project and move the appropriate files. Make sure to update the DESCRIPTION file if the old package needs functions from the new one. If each package depends on the other, that's a sign you need to refactor.
As far as Git, I have no idea how to best split a project. I want to say clone the original for each of the new projects and keep their future histories independent. But having two non-linked projects with shared history is raising the "there's a better way" flag in my head.
Have a deprecation warning print when somebody loads the to-be-abandoned package (see ?.onLoad). Point them to the new packages.