Hi Peter, I've got a JMI focuser. The GPU sits flush with focuser tube and neither protrudes into the main tube when in focus. I'll get photos for you in the daylight.
For collimation I read the manual
https://manualsbrain.com/en/manuals/1387484/?page=41 and this full setup guide
http://www.weasner.com/lxd/techtips/..._Newtonian.pdf to get the general idea of what to expect. I then used an OCAL and a flat panel to do the basic setup. Then a star test. I did have to use an offset in OCAL and I've later read that is a problem so I will be redoing it including the final step with a cheshire which I impatiently skipped.
Cheers.