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.

Management decisions that are relevant in determining whether you actively participate include approving new tenants, deciding on rental terms, approving capital or repair expenditures, and other similar decisions.Remember, if you qualify as RE professional, there is no limitation if you materially participate in your rentals.

NOTICE: If Landlord fails to repair a condition that materially affects the physical health or safety of an ordinary tenant as required by this lease or the Property Code, Tenant may be entitled to exercise remedies under §92.056 and §92.0561 of the Property Code.span>If Tenant follows the procedures under those sections, the following remedies may be available to Tenant: (1) terminate the lease and obtain an appropriate refund under §92.056(f); (2) have the condition repaired or remedied according to §92.0561; (3) deduct from the rent the cost of the repair or remedy according to §92.0561; and (4) obtain judicial remedies according to §92.0563.

Because I have such a long time before rehab starts I plan on buying a lot of my materials and such on FB Marketplace and Craigslist. 

Don’t have much experience with odor issues, but sometimes enzyme cleaners work well because they actually eat and dissolve the organic materials.

As will construction materials, and original construction workmanship.

Or is it better off to go with a private contractor, and just pick out the materials myself?

I've sent you a connection request so I can send you some materials on that topic.