Sounds like your house is around 50 years old or so.
Q#1:I like to run 18/3 wire minimum, you have an extra line in the jacket for future or if one of the lines break.
Q#2: I like to use 3/8" flexable metal conduit around boilers and fasten them appropriately. Sleeving the thermostat wiring to control boxes. On the zone valves I take a ball point pen, wrap the t-stat wire snuggly around it. Makes a shock whip, looks like a short telephone cord when your done. I make these about 4-6" long just before connecting to zone valves.
Q#3: I don't know your local electrical code or fire department codes but mostly I run a feed from the panel to kill switch then to the boiler. The switch should have a gas boiler switch plate thats red at the last or first door before entering the boiler room or basement. I also install another switch on the boiler itself for servicing. This is a gas system so no fire-o-matic is nescessary.
Q#4: When applying the feed to the boiler run emt up to the ceiling and make a 90 degree bend, bring the conduit away from being directly over the boiler and acssesable.
Q#5 I'm not sure of this honeywell item.
I know mostly that circulator pumps are better than zone valves.
