1. Was it possible to replace the fork without removing the transmission?
No. Engine or gearbox out.
2. Is there a better replacement fork. Why would a fork fail? Seems odd to have that be a weak link.
Get an OEM fork (not an aftermarket one) and weld on a backing plate, being careful not to overheat the pivot area. Grease well.
3. OEM clutch fine? This is a daily driver - farm truck and not a rock crawler application.
Sure. I'd replace it...
4. OEM rear main seal - is this the best option.
You want one of these: http://www.turnerengineering.co.uk/a.../info-832.html