When I fitted the chain to the Spearfish I did the usual big to big + 2 links, but I can never remember if a link is one bit of chain or the two bits, so is a single 'link' the a narrow and wide section of chain together or just either of them? I think I have added 4 links as I thought it was the narrow/wide together.

The chain does look like it could be shorter? Here it is in the two extreme gears





It also seems quite noisy in the lowest gears, especially under load. The chain and cassette were brand new but the chainring has done 830 miles. The chainring doesn't look work but could this be enough to cause the noise? It can also be heard if I spin the cranks backward at speed and it does sound like it's coming from the chain as it leaves the chainring.

And finally, the chain occasionally skips when in a middle-ish gear, it might be it was trying to shift and then re-seated. I noticed it most once the drivetrain was muddy. I think the indexing is right, the gears shift instantly and crisply in both directions. Is this just something that can happen from time to time with 1x11? Previously I've only had 10 speed which didn't seem to suffer like this.

Apologies for all the questions, my normal gearing is easy, chainring/chain/cog and just pedal it along or get off and push

My initial thoughts are is the mech hanger bent ? Only needs to be out a bit and your gears are dancing like a drunk at a disco.

Don't want to ask you to suck eggs etc. But did you also replace the cassette ?
Imo the chain length looks fine.

The chain and cassette are brand new. The mech hanger is a good shout. It's bolt on and I have a brand new spare I could swap over to test, plus the frame was pained so there is a possibility that the hanger isn't perfectly parallel to the axis of the cassette. I think a friend has a checking tool so I can borrow that so check.

Had similar when I changed my cassette & chain - middle gears skipped a bit. The mech question was answered for me - 2 days later the arm locked solid. Bunged a new one on and it's super smooth now. Probably different situ to yours but interesting coincidence.

The mech hanger is a good shout by gregsie.
There is also a possibility of the top jockey fouling the cassette sprocket on some gears causing excess noise. If so,screw the b-stop screw in clockwise untill it pulls the jockey and chain away from the sprocket slightly.

Sean... i think you've been away from full sus for a long time did you remember to ensure the rear shock was empty of air and thus extended the chain length to its full max... I reckon it'll take another 2 links (1 inner and 1 outer) once you fully extend and thats most likely your problem...

Sorry if you've already done that and dont mean to teach you to suck eggs (but sometimes a reminders not bad is it )

Judging from your second image Sean, it seems you've got a case of too short a chain (but the problem might be more than that and I'm sorryif it is). On top of that image if you was to sit on the bike and full force down (full extension) it'll probably show up as even more evident...

Hope that helps