I don't think the guide pins were supposed to come off with the pressure plate. When the surface is re-ground, the machinist would have to remove them anyway, so take the pressure plate with you so s/he can re-install them after resurfacing.
Problems you face are breaking loose the large funny-headed bolts that screw into the end of the crankshaft. The crankshaft will want to turn while you want it to stay still. The only blocking mechanism I can think of are 1)strap wrench around the front pulley or 2) using a breaker bar on the bolt in the nose of the crankshaft braced against the frame to hold it still. The flywheel is also heavy, so don't put fingers or toes in its way if you happen to lose control. It will sit on the end of the crankshaft, but don't rely on its staying there without a 'helping hand' to steady it.
When you go to put it back, be sure that you don't get grease or oil on the machined surface or you'll be back doing it again soon as a contaminated clutch will grab erratically and you won't be happy.
Some flywheels are supposed to be installed in one way only. Check to see if there are marks or different bolt alignments that indicate the flywheel should go on only one way. I think the bolt pattern may be slightly eccentric, forcing you to put it on only one way. I haven't done a clutch in years.
tom