Day Eight
When cleaning shock I noticed a mark obviously caused by it coming into contact with something repeatedly. 
So I reassembled everything with loose bolts to see the cause. Was expecting it to be when bottoming out but it was the opposite, when it tops out. The Nitron shock is 5mm longer than OEM so that would be causing the issue. (Length difference and slightly less travel also contribute to losing 10% of my precious suspension travel, another reasons I wouldn’t recommend it.)
The clearance issue seems to only be a matter of one millimetre so when I come around to putting things back together I’ll look at using the slack in the mounting bolt holes to try and gain an extra millimetre, a little filing wouldn’t go amiss either. (Metal removal is on the low load extension side, not the side exposed to the high compressive load of bike weight and potholes.) I also intend to put a bit of paint on the surface to act as a witness for reoccurrence.
Anyway, the original aim for today was to get swingarm out so I whipped off the wheel spindle nut, took up the wheel weight on the jack and expected to wiggle out the spindle, no such luck. After a bit more wiggling, and a light tap with a hammer is still wouldn’t budge, not had this problem before. 
After wondering a while what I might have forgotten and not coming up with anything I could only think it was stuck with corrosion. Then I remembered that the last time this wheel came off was when the muppets at the Scottish tyre place fitted a new tyre. They didn’t even refit and test the brake caliper properly, and they certainly wouldn’t have cleaned and greases the spindle and bearings.
The only thing I could think of was to use a big hammer, but it occurred to me that I didn’t want to be forcing any extra muck through the hole so used neat bike cleaner on all the gaps between parts, then after a while rinsed and brushed on paraffin to clean and flush out as much grime as I could.
With a block of wood over the spindle end to protect it I used a 3lb lump lamp hammer and gave it a couple of good whacks. It still didn’t budge and I was getting concerned, but I couldn’t think of anything else to do. Now I resorted to successively bigger slings with hammer, at one point slipping off and putting a ding in the swingarm 
Eventually it moved, and after a centimetre I could get a spanner on the other end to twist spindle back and forth whilst tapping gently with hammer the other side.
When there was no spindle left to hit I found a bit of wood dowelling to drift the spindle out completely.
Yep, spindle has corrosion.
As does the bearing race.
I always make sure these surfaces are clean and well greased when I have wheel off, so to get that corrosion it makes me wonder if they wiped off the old grease. I blame myself for not having the wheel off after getting home to check things.
With all the hitting I’d done I only now got to thinking about what damage that might have caused. The rusted and stuck bearing race would have had high sideways force, but should have been supported by the spacers against the swing arm. Hopefully swingarm itself was up to the hammering.
All the wheel bearings felt smooth and had no play, so decided I wouldn’t replace them. (I did them last 2 years ago.) I wanted to clean the corrosion off the bearings and the spacer tube between them, but I was aware that any abrasive would shed fine particles, and even with sealed bearings I didn’t want to risk bits getting in. So instead things just had a good firm rub with a stiff finger wrapped in a paper towel then gave the holes a good greasing. 
Spindle took 5 minutes with a Scotchbright pad to get cleaned up before greasing.
I then set about doing my usual wheel removing cleaning, like cleaning the thread on the wheel nut by twisting it onto an old brass brush, and using 1000 grit wet-and-dry cloth to get corrosion off washer and other flat surfaces that mate together.
By the time I had done my second run over the sprocket carrier and cush drive with paraffin, then washing up liquid, my finger and wrist were complaining of all the cleaning and scrubbing work they were being subjected too so decided that was enough bike work for the day.
The seals around the wheel spacers had a fair gap so I’ve just ordered replacements from Simply Bearings, they probably contributed to the corrosion. Normally when fitting a tyre I liberally grease the seals and the space behind them, again, not something tyre fitters would have done.
Edit: After sleeping on things I’ve also ordered new wheel bearings, I knew it’s the right thing to do, it was just that after a week of working on bike with many more days to go I was hoping to avoid even more work.