The plan is to have a completely open source toolchain from the HDL to P&R.
https://github.com/haojunliu/OpenFPGA
https://www.synflow.com/#home-Synflow
http://legup.eecg.utoronto.ca/
The Leon3 GPL SoC might also make a good test case for you since they're designed for easy customization. Lots of academics use it for experiments.
http://www.gaisler.com/index.php/products/processors/leon3
https://github.com/haojunliu/OpenFPGA
https://www.synflow.com/#home-Synflow
http://legup.eecg.utoronto.ca/
The Leon3 GPL SoC might also make a good test case for you since they're designed for easy customization. Lots of academics use it for experiments.
http://www.gaisler.com/index.php/products/processors/leon3