I would like to help but I am a little bit confused with the sequence of steps that you are taking.
Maybe you could collect them all in a script-like form and share them?
The basic idea is to boot your db410c with a not too recent Ubuntu/Debian release and then replace the kernel and install the Xenomai libraries.
Do you know how to replace a kernel in a Ubuntu/Debian release for a vanilla kernel? That should be your first step, ie, making sure you know how to do this standard operation.
Now back to installing Xenomai: when replacing the kernel you can either use the same kernel sources that you are booting patched with I-pipe OR use an I-pipe enabled tree (which is what I do in the document for simplicity). An I-pipe enable tree is basically a vanilla kernel patched with I-pipe (so not a Landing Team or a silicon vendor tree features there)
Once you have the I-pipe enabled kernel you should boot it to make sure I-pipe is not introducing a regression. If it is all good - the system boots- then you have to patch the kernel again this time with Xenomai (ie prepare-kernel.sh script_
==> So to be very clear: the I-pipe enabled tree MUST be patched with the Xenomai domain (hence the prepare-kernel.sh).
After that you would just boot it and install the Xenomai libaries as per the documentation.
So if you could help me understand where are you getting stuck I should be able to help.