I watched Brandon's youtube video using the 4 square method and my CoC Return was 40.4% vs using the excel spreadsheet punching in the same numbers but coming back 10% lower.

You have a city that's 7x7 where it's not easy nor much space to build on, w/ a demand for folks wanting to get into the tech sector.

I recently started a Civil/ Structural Engineering Firm in Portland (we are also branching to Tacoma, Washington) If you have any up in coming projects please let me know I would love to work with you.  

Do I compare the building with a single story home of similar square feet?

Other stuff like out of square walls and doorjams with the sheetrock proud of them you don't notice till you're working there. 

I have spent close to $10K with them already this year so I should have looked into it before, but I'm re flooring (carpet in bed rooms vinyl or hardwood in the common areas and leaving the quality tile that is already in the bathrooms) a 3100 square foot two level home this month.

@Josh Cohen - Bigger Pockets has two great books that can be found here - The Book on Estimating Rehab Costs is a fantastic source of numbers, while The Book on Flipping Houses is a fantastic source of strategy.I believe that you can get them in PDF form or hard copy from either BP or Amazon.To give you an idea of what the first book has - an example page is for flooring, where it will go over all of your options (laminate, hard wood, tile, etc) with cost per square foot, installation cost, comparisons for how long each option will last before needing to be replaced, etc.

I toured one of the largest log homes in the US near Seattle WA.

You utilize these comps to figure up an average per square foot sold price and then use that figure to determine your ARV.The best way to get comps is from the Multiple Listing Service (MLS).

Really big square tiles that make complete pattern.