The build you linked is a PvP build. You should probably consider looking at some more PvE focused builds while you're getting through the campaigns.
Use the new PvX wiki if you're looking for build templates -
http://www.gwpvx.com/Main_Page
1) when am i in "main game"
In factions, once you hit the mainland after completing Zen Daijun.
2) him being a PvE character, will he still be able to aquire skills from nightfall, being that he is from factions
Yes, you simply have to complete the quests to travel to the different campaigns. The Faction's quests to travel to Nightfall/Prophecies/EotN begin in Kaineng Center. There will be a popup each time you zone in which directs you to the quest givers.
Skills are the most important part of GW. You should aim to be able to make several different builds for different situations and to keep the character interesting.
3) will he be able to get armor from nightfall being that he is from factions?
Yes, same deal as skills. Do the quests to travel between campaigns and then progress the storyline, you'll find armor crafters a long the way.
4) as a PvE character, will he be able to get a defensive set/zealous daggers, or are those strictly for PvP characters?
You can get all the items available to the a PvP character on a PvE character. You can get weapons from collectors, crafters, drops or buy them from other players. To get perfect weapons, chances are you will have to trade with another player to either buy the weapon itself or the mods to go on it.
5) will i find armor smiths in other citys as a travel through "main game" that can supply me with good enough armor (when i hit level 20)
The first max armor crafters for Factions are in Kaineng Center, after that you'll find various crafters throughout the campaign(s) which offer to craft armor with the same stats which simply has a different appearance. Armor is essentially chosen for which you think looks best (you can check out all of the various styles on the wiki -
http://wiki.guildwars.com/wiki/Main_Page).
xPc.