Alexander Rössler has put together a page showing how to create a Machinekit image for the BeagleBone based on Debian Packages.
The current packages still require absolute paths to the PRU code in your configuration files (sadly, a different path than is needed for the previous run-in-place builds). I hope to have enough time to address that soon by embedding the PRU code directly into the HAL driver. This will also prevent any possible confusion caused by the HAL and PRU code versions not matching (which I can confirm is a nasty issue to track down if you're not looking for it!).
Package installs also make it much easier to update both Machinekit and the kernel, both of which are "difficult" to update on all of my currently available images.
If you feel up to the task, I strongly suggest switching to a package based install. It should make it much easier to track ongoing progress with both Machinekit and newer kernels.