Firstly, I'd like to say that it is super nice of you to offer to personally help me!

It is a very nice gesture and is it much appreciated. Unfortunately, I live a ways north of you, in the Macedon Ranges area. I wouldn't even mind bringing the car down but, as of right now, the car has no rego. My mate (who owns the Polo) is waiting on a pay-cheque to purchase a month of temporary rego. I keep badgering him about getting the temporary rego as it makes it difficult for me to work on the car without being able to drive it. So yeah, for the time being at least, I can't take it anywhere...
As for answering your questions:
1) The timing seems to be ok to me. I'll check it again, more closely.
2) Injector short to open I seriously think was from someone doing previous testing. And now that I think about it, it may have even been me, when I very first popped the bonnet and felt the misfire, I think I unplugged the injector. The fact is, once I cleared the codes, not a single code has returned that hasn't been as a result of my intentional unplugging of things for testing purposes. As the car sits and runs now, there's no codes.
3) Can I feel the misfire on 2? Without a doubt. And if I unplug the injector to any of the other cylinders (1, 3 or 4) then it REALLY starts to miss. If I unplug the injector to cylinder 2, there's no difference at all. HOWEVER, if I swap the oil-gunked plug with, say, cylinder 4, then the misfire in two goes away and there's a misfire in 4. That is, until enough oil starts to accumulate in the plug in no 2, at which point it starts to miss there again. If I then remove the plugs from 2 and 4 and give them a good clean up, and put them back in, then the engine purrs like a kitten. For a while, until no. 2 gets gunky again. It doesn't happen right away, either. Which is what makes me think it takes until oil vapour begins to build in the crank case and has no where to go and so starts to shove up past the piston rings. Like I said, ALL the electrodes are pretty dark. It's just that 2 is the worst. At least the others are all dry and there's clear signs of where the spark is occurring on the centre electrode. With 2, it's just oil. At least the other ones are still firing. As an aside, I pulled apart the dizzy cap and rotor arm and used some sand paper to scuff up the contact points and get the black scoring off them. I was pondering whether a weak spark wasn't doing enough to burn off the carbon deposits on the plugs. I am currently awaiting arrival of the replacement cap and rotor. I Ohm-meter tested the plug leads and they tested ok. I sprayed water around them at night and saw no sparking/arcing.
Now, not to insist on being spoon fed the info here, but I can only see one fastening bolt on the underside of the black PCV box. Is the other fastener wedged up under the intake manifold? And is the best method of action to somehow remove the breather hose first, then remove the black box? Or is it better to remove the box and take out the unit as a whole, and then disconnect the hose once it's all out?

Because like I said, I have huge hands and can't get any kind of a decent grip on the hose as it stands, certainly not a grip which would afford any sort of dexterous manipulation of any tabs or clips. Grrr...
As for the thermostat in the air intake routing door, I don't reckon that works. It only ever routes hot air, so yeah I'll definitely disconnect that end and then re-attach it for roadworthy.
Now, on to the latest and greatest as this project transpires...I'm embarrassed to even write this but....I sheared off the centre bolt holding the valve cover.

I honestly don't even know how it happened. I fastened the outer two and they went on until they tightened down. Then I went to finish tightening the middle (i was doing them in succession, bit by bit for an even torque across the gasket) and the middle one just wouldn't really tighten. So I kept spinning and then SNAP!. Ugh...so embarrassing...So now I'm trying to decide how to get the broken bit out of there. It's way down in there so there's no hope of using pliers on the stump or anything. I'll need to drill it out, I suppose. But that leaves me concerned about getting metal shavings inside the head. I would obviously tape off the area and just have that bolt tube exposed, but yeah. I'm not experienced with drilling out sheared off bolts and am quite terrified of running at an angle and thrashing the threads on the head-portion of the bolt hole. Ugh. Like I said, embarrassing. I've never done this before. And obviously, I'm going to need a replacement valve cover bolt to replace the broken one, once I manage to get the broken one out.
The reason I opened the valve cover was two-fold. Firstly, I wanted to get an idea of how dirty it was in there, as the area in the oil fill cap was sludged to all hell. As it turns out, it's spotless in the head and I reckon the valve cover is secondhand. As to why, I have no idea...
The other reason is because I was curious if the head bolts were torqued down quite sufficiently to the engine block, as there seems to be a slow-but-steady weep of oil from around the entire front side of the head gasket. And recall that the head gasket was changed not that many kms before I got to the car. I'm wondering if that slow weep is normal. But alas, the head bolts are not normal bolts - they're massive torx bolts, which I haven't got. I'm not even sure of the size of them or I'd go buy one...
So I really want to give the car all the TLC it deserves: full fluid and filter flush/replace. Repair interior (the door cards have some holes in them, the passenger side sun visor is broken off and missing, I need a new mirror cut to fit the passenger side mirror, I'd like to wire up a set of rear speaker but hey, at least I was able to pull out the head-unit and get the serial number to get the unlock code!), respray exterior (the entire clear coat is just...gone). And honestly, the work I have done so far HAS made a noticeable difference in how she runs but...my initial approach was that, until I sorted out the misfire I was going to hold off on all those fluids and filters. But now this sheared bolt...ugh...
Once again, if you've read this far then I thoroughly commend you. I have a nasty habit of writing WAY too much. But then I figure, once I spent the time writing it, I'm gonna post it...
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