I've been meaning to provide an update for the for a while so here goes.
I still haven't fully resolved the issues with the controllers but I've not really had a good stab at it yet.
A few more photos; generally I'm happy. When reassembled the fan blows straight across the compute module (which was the idea) so adding a heat sink so keep it nice and cool.
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The HDMI port in not fully aligned - not a major problem but the perfectionist in me doesn't like it - that on the list of changes if there's ever a next version. Also, I'm not too keen on the empty hole to the right, might be an idea to add another USB port in future.
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Front USB port fits nicely into a slightly modified memory card port but doesn't sit at the correct height - something else to be tweaked.
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As for the next version, this is on hold for now. One of the original aims for using the Compute Module was future upgradability base on the assumption future Compute Modules would keep the same interface/footprint. The ultimate hope was the come CM4 or CM5 the power might be there for GameCube emulation.
However, I've read that future versions might deviate from the SO-DIMM 200 interface, hence I'll hold off on making any more hardware changes with this until there's more clarity on what the future holds. It's been a fun process and has taught me a lot on the way - which was the real aim anyway!