1+2) I'd go for replacing just the one piston, but pull them all to inspect/measure clean grooves etc. You'll know what to do from there.
And install all new rings.
3) I forgot the pros and cons of stone hone versus dingleberry hone.
Used to know. But i've always preferred the stone hone. And since you have one ...
You control the cross hatch by how you work the tool up and down.
Slower is less degrees of cross - faster is more degrees.
4) No idea on swap. But the cam is hardened surface on lobes, a good effort with naval jelly and 000-0000 steel wool might could surprise you. The non critical areas could be cleaned with wire brush on drill - or similar.
Or perhaps could even have it thermal baked/cleaned at a shop such equipped.
5) Yes absolutely could be, but they probably addressed any factors like that when rebuilding the head.
6) Check operation of Gplugs while you're right on top of them.
Clean/lap the Injectors and install new heat shields.
An injector rehab link if you need it:
http://vincewaldon.com/index.php?option=com_content&task=view&id=20&Itemid=287) Verify piston protrusion - replacement(s) versus existing(s) after assembly and cross reference to the head gasket you have.
8 ) Pre-prime Inj Pump with ATF and let that soak for a day or so.
Rotate some by hand or air tool so often.
9) Welcome to a great forum. I'm new around here too.
But not necessarily a soaking wet rookie.
If all goes well on job, and the odometer was still working, at only 140,000+, another 200,000+ should be in the future. My 89 Jetta ME is over 340,000 and still daily driven with excellent MPG.