re:   you will  have a lot of trouble putting the cylinders back on as
they will NOT slip on the piston rings and there is no real way to get
a ring compressor in there

I have not seen a torn down waterboxer engine but can offer that there
are piston ring compressors specially made for the instance where the
cylinder slips over the piston.  This is common in aircraft engines
and I have one for my BMW motorcycles.    All it really is is a
compressor that easily dismantles.  Got mine (two different models)
from Snap-On.