Still doesn’t add up to me so I’m going to hafta try and find out what really happened to all the money by getting contractor to send me invoices and receipts for material and try to reconcile that to bank account statements.  

It's hard to beat much of the free material on this website and the books published by Bigger Pockets for that introductory glimpse.

I am looking for any recommendations for a general contractor that I can use on all my future jobs that is reliable and investor friendly when it comes to materials and cost.

@Idan Narotzki Careful screening, strong lease (and strong enforcement of it), diligent move-in/move out checklist (so they know you’re paying attention), large security deposit (I ask for double 1 month rent amount which in my area means $3-5k), avoid Class C-/D, find a good collections agency that will work on contingency basis, make your units as tenant-proof as possible with inexpensive yet durable materials, hold plenty in reserve funds, set proper expectations, communicate well but firmly and treat tenants fairly and professionally, and be willing to clean up a mess and fix things occasionally rather than pay a company thousands to do it for you.

What is the proper way to add materials I purchase for the home build to the cost basis of the home, especially if I buy them before a.) breaking ground or b.) a calendar year before the home is finished and sells?

Here is a checklist for Getting Bids for your Project.Create a detailed Scope of Work for your ContractorsCreate a material list and define who is responsible for materials (you or Contractor)Finalize project drawings (if necessary)Call Contractors and schedule contractor walkthroughs to receive bidsEvaluate contractor bids and determine the Lowest Qualified BidderAward contracts to ContractorsRehab Prep After you receive Contractor Proposals, you need to finalize your Project Budget, Project Schedule & prepare for closing so you can 'hit the ground running' once you close on the property.

In one of my groups, a condo owner has received a notice from the HOA board:"Unit owners shall be responsible for painting their limited common elements (earlier defined to include interior walls, wallpaper, and flooring); provided, however, the color, materials, and design of limited common elements may not be changed without the prior written consent of all the Unit Owners."

I don't know (recall) if they are in local ordinances but I do recall vaguely seeing some legal / ordinance type of material detailing when it can and cannot be done, regarding building in a way that directs water towards a neigbors property.I don't know Chicago that well, but as a homeowner I would try calling your local building and permit center and see if one of the local inspectors can direct you to the code section to read.I'd do that before anything else because knowledge of those ordinances will arm you / prepare you best to approach the other parties.With regards to the possibility of 'dealing' with the water, I'd be thinking about ways to do that, too - in the event that the above / negotiating an alternative solution is not fruitful. 

(Both dad and I will use cash to purchase materials) we will both be the laborers and sub out roofing, drywall etc as needed.

That is the first thing that college students look to for housing.As far as the property itself, my suggestion would be to install wear resistant materials as units turn because with students you get more wear and tear than normal tenants.