We did know he had made alterations to the unit before we closed.

CPA's, Tax advisors, Landlords and House Hackers are more than welcome to chime in.Here are the questions:  Since there was an existing system (that will be pumped, crushed, and abandoned), would there be a difference (deduction/depreciation-wise) if this is considered and alteration vs an install?

That would alter your numbers. 

On larger properties, outside of performance calls, owner's usually get involved if there is a big bust in the budget (to alter the business plan if needed), capital expenditures are going to be more than estimated (find ways to cut costs if possible), or leasing strategies need to be adjusted to keep up with other competitive properties (example: providing concessions on new leases or renewals). 

However, IF INDEED YOU ALTERED THE OFFER, you DO NOT have a ratified contract.

In my services I will attempt to grab as much real data as possible, so I will call  utility companies, and look at the market data, and I will alter the analysis based on request.So my question is this something  potential investors might be interested in?

Now obviously I know that a roof/furnace would alter this number, but overall it's a huge gain.401(k):Now assume that I take that same $18,000 that I used for the rental property but instead max out my 401(k).

(C)   Tenant shall not make any additions, improvements, or alterations to the Premises unless prior written consent is given by Landlord, which may be given or withheld in Landlord’s sole and absolute discretion.

My tenants are not allowed to alter anything without my written authorization.  

Write in whatever you want (ie tenant can move out anytime with no penalty with X days notice).If you're not comfortable altering or adding lease language for that, like Wayne Brooks said, just do a mo-to-mo or week-to-week lease.Curious though, from an owners perspective, why would you want to give the tenant an easy out?