Here's my HQM guide for Refugee to Regent:
https://dl.dropboxusercontent.com/u/37766763/MC/R2R_v1.0.zip
This is made to work with the FTB Infinity Modpack (v1.4.1). Inside you will find the configs, tweaked a bit for the challenge, as well as the HQM quests with my interpretation of the challenge.
Currently it only guides to the redstone stage, but if there is interest I'll complete it. Let me know what you think!
The intro text was quite good.
I think you have the essence of the challenge pretty much there, but (in my opinion) you rely a bit too much on the honor system. Up to the point where you have them gather wheat/carrot/sugarcane/potato/oak/planks/saplings I think was great. When it started to go sideways for me was when you'd just turn in a piece of dirt or a plank and get a pack full of saplings or something. It's good, but I think the turn-ins should be a little more tied to the task. Like require the player to possess clay (gathering task) rather than a turn-in. Or if it was more mod-specific, have it detect when they've crafted all the basic tinker's stations. No need to reward them with items - just give "Reputation" for each age. Let later ages unlock when a player has reached a particular reputation level in the previous age.
It's definitely better than some of the attempts I've seen. Good work!