The core of eclim is a server that talks to the Eclipse JDK, for which there are vim, emacs, etc, front-ends.
Eclim also happens to provide an Eclipse plugin that _embeds_ Vim in Eclipse, using the NetBeans protocol, just as you are embedding Vim in Sublime. The author of eclim is also very responsive, if you wanted to ask him about anything.
Is he not just embedding a VT100 emulator and using NetBeans socket to copy the buffer back and forth? The primary focus of NetBeans integration is to pass basic state forth and not to facilitate a full Vim embed.
To be honest, I don't know. An eclim discussion implies that eclim is using Vim's NetBeans protocol, and the eclim code that I have read is well-organized and the project is mature, so when you said you were having issues with the NetBeans protocol I thought eclim might be a useful reference for you.