Just to finish off my account and add a few more details...

I've managed to clear the EML fault code - I tried a cheapy dongle from Amazon (EM327 with Torque OBDll app) but could not get it to stay bluetoothed to my phone. I got it to work on my wife's VW Up! - so I don't think it was user error. It wouldn't communicate properly with my Golf GTD either, so I gave up on that and will send it back to Amazon.
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Then I went and bought a "Streetwize Car Diagnostic OBD II" tool from Toolstation and that worked within a few seconds at finding and cancelling the fault codes (which showed up as a throttle sensor issue amongst a couple of others - I should have been more diligent at making a note of them but got carried away wanting to see if I could cancel the light!)
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My conclusion about what had happened to cause the EML is that I was daft enough to switch on the ignition while all the connections were unplugged when I was working on the valves and the manifold was off - and the ECU had a fit about lots of things being missing (throttle body, knock sensors, coil packs). But as soon as it was all back in place and the light was cancelled it was happy again - I've just driven back home 15 miles with no problem.

It may be some kind of wishful thinking/placebo type effect but the car seemed livelier than before, so cleaning up the valves may be helping it breathe more easily and maybe producing a bit more power. It would be interesting to take it back to the rolling road I used a while ago to see if it is any different, but I'm not sure I can be bothered as it's a couple of hours drive away from here.

Re the request for a diagrammatic of the breather system - I have no idea, but the top hose from the cams to just before the throttle body is very clear to see and understand. The other "guilty" one from the crankcase to the inlet manifold is very short and deeply buried behind/underneath the inlet manifold. Here's a screen grab from Robert's video:
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As Dave has already recounted, the only end you can reach with the manifold in place is the connection to the manifold and that is out of sight and tricky to disconnect, but not impossible. It's a squeeze the textured side tabs of the clip and pull straight off - there's no give in the hard plastic hose to twist it off.

I'm hopeful that there will be no further build-up of oil/burnt-on oil/carbon on the valves now that I've diverted the crank breather to an oil separator and then to atmosphere. As others have found there seems to be little to no oil coming from the top breather, but in order to monitor things I took the opportunity of the manifold being off to create an "inspection port" in one of the inlet tracts close to the head, where I can poke the endoscope to get a look at one pair of valves in the future, without having to take the manifold off. It's a stainless M10 machine screw cut down to just a few mm long so similar to a sump plug, screwed into a tapped hole in the quite thick plastic of the manifold, with an O ring to ensure a good seal. (probably sacrilege to some, but it's my car and I'll do what I like with it!)
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Keith
2017 Plus 4, deep blue