I finally got round to cutting a big hole in my AV rack so the Onkyo can fit inside. I have fitted the door, it all looks tidier now. The sub is on a slab of marble, and the speakers are back on spikes and tiles. This is mainly to make the shop downstairs life a little better, although the slab under the sub did tighten things up nicely.
Best upgrade to my system ever has been my recliner! Never under estimate comfort on your systems sound quality. Picked up a harmony one as well, like it a lot.
Positioning isnt ideal because of the mantle, but it sounds alright. Thanks to the carpet and high ceilings it actually sounds better than my old house.
A number of comenters suggested isolating the centre speaker, and I've half done it. I cut a bouncy ball in half and put them under the front of the speaker. I did this to angle the speaker upwards more towards the listeners ears.
Finally, here is the whole I cut in the back with an enormous amplifier hanging out...
Turns out I didnt need to reinforce the centre column, it was plenty strong enough even with a 3" by 7" hole cut in it. Think that about covers this update.