Let me reiterate what I understand from your question. Your project is huge and minor changes to a layout result in crashing - owing to rebuilding the entire project. So, you want to know how to build only a part of the project - with the R file instead of rebuilding the entire huge project on minor changes, which crashes.
What you can do is, uncheck the "Build automatically option", make your changes and build manually once all the changes have been made, instead of building the project on every saved change.
I don't think you can generate only the R file since it needs to read all the res files and generate ids for all the resources, excluding none...I don't think that can be done in parts.
There is a way to generate the R.java file from your resources using the Android Asset Packaging Tool (aapt) as stated here (thanks to Pearl for the pointer)