www.linuxcnc.org is a retrofit and they say they have support for all you are saying. What kind of accuracy are you looking for? A boss 4 will need to be totally rebuilt for improved accuracy. If it is running with the old control you would be better off trying to use it. If not mistaken, should have accuracy and repeatability of .001. Be warned, retrofit and a little money don't go together.
www.geckodrive.com also has encoder feedback on some of thier stepper motor drives. That would make sure it would not skip using the right software.
Steven