I don't know what kind of materials or product I need to finish this wall, and because of flooding how much time I should give it to air it out.

I have some experience in certain areas and some knowledge regarding tools, materials, and processes.

The obligation of Lessee shall indude the repair or any damage occasioned by the installation, maintenance or removal of Lessee's Tra e Fixtures, furnishings, equipment, and Lessee-Owned Alterations and Utility lnslallations, as well as the removal of any storage tank installed by or for lessee, nd the removal, replacement, or remediation of any soil, material or ground water contaminated by Lessee, all os may then be required by Applicable Requirom nts and/or good practice. lessee's Trade Fixtures shall remain the property of lessee and shall be removed by lessee subject to its obligalion to repair and resto o tho Premises per this Lease.Actually I just cut and copied this from the lease (OCR so the text came out poor) it looks like they get to keep their trade fixures.

VA guidelines require that “The surface requiring treatment must be thoroughly washed, scraped, wirebrushed or otherwise cleaned to remove all cracking, scaling, peeling, chipping and loose paint and then repainted with two coats of a suitable nonleaded paint, or:The paint shall be completely removed or the surface covered with a suitable material such as gypsum wallboard, plywood or plaster before any painting is undertaken if the paint film integrity of the surface needing treatment cannot be maintained.” 

I would wait 24 hours of low spore count before continuing work.Buy different color bags for mold material.

I get materials delivered on site so my foreman doesn't have to get them.

I would suggest either a high quality asphalt shingle with a Lifetime warranty (50 years material, up to 25 workmanship guarantees) or a natural slate tile.

Of course pricing depends on the materials used, but still we'd like to have an idea about what is reasonable. 

When pulling out the old carpet, I got the carpet and a middle "pad" type material out, which had the majority of the pet smell in it.  

@Jon Gorham Student housing can be a great investment just make sure that you use really durable materials (high traffic carpets, stain resistant paint etc) to help the house stand up to the potential beating it will take from the tenants and remove things that break easily or increase your liability (IE ceiling fans).