I have a background in engineering and survey and my wife has a background in architecture design.

@Hunter Woolsey  You might check the architectural salvage place near Love Field. 

He built the modular portion of my house in 2016 and I have referred him to a few of my architecture clients.

If you don't have a background in construction / engineering / architecture I would not try and GC your own house.

This is standard architectural shingles, ice and water up 3' to code, felt, shingles, ridge vent, drop edge all around, new boots, flashing at chimneys and walls, no soffit work.To get close on roof SQ find he perimeter of the house dimensions and get the SF of that (not just house SF as two stories, added garages etc all factor in). 100SF is a Sq and that's how roofing is usually priced.

Architecture is next with a license.

It's cost is significantly less than 400k (including the original architectural fees), but I was under the assumption the assessor would give a high target value due to the area the ADU is in. 

You will need architectural drawings to file for building permit.

When comparing architectural bids, what key items should I be looking for?  

You can get older growth recycled flooring at various architectural salvage places.