I cannot answer all of it, sorry.
Regarding knocking the crank no, you cannot knock it 'in' like that, it will not be out of place
Regarding turning the injection pump and the high pressure pipes. They will not (unless you are unlucky) be like easy snap brake pipes , they are a bit more hardy for obvious reasons.
You should slacken the nuts (at both ends) a couple of turns before attempting to move the pump to avoid straining the pipes. You can get a proper spanner for it (think of a larger version of a brake pipe spanner) , you do not usually need to remove them completely, just undo them a couple of turns. A small dribble of fuel will probably appear even after all this time of non running, do not be concerned about this.
Having said that, if you are going to turn the pump a fair way, its probably worth taking them off.
Just wire brush them and plusgas if you want.
I've never tried to move the pump with the pipes tight. Jim will have to advise if he meant locking it all up and then trying it, slackening off , moving , tightening up and trying again etc.
Obviously they need to be secure before you attempt to run the engine.
Set the pump about in the middle. I would guess its fully one end as that was done due to the timing being out by one tooth, a kind of way to compensate for it. Ensure its in its proper place (pin wise)
I would not be really concerned regarding the one pin in and one not quite, as I say mines like that
You will 'feel' a bit of resistance as you turn the pump anyway by hand, remember it is a pump after all, so you will feel something.
Not sure about freeplay in it, very early (pre 86 maybe?) pumps had a modification of a dust shield fitted behind the sprocket area (or there abouts) to stop dirt getting in and ruining the front pump bearing. Unlikely to be your issue.
Hope that's a bit of help.