if the contractor is doing the complete job he should be giving a discount, not charging for market pricing for every specific item.

I would still want those other experience points, but I would want to see this specific item as well.

Either way what ever you do you need to have a focus on a specific item class, area, and exactly what you want.

@Laden Brooks III -  Still "patiently" looking- Has a system for how he calculates the costs for specific items/jobs. 

Here is that specific item in the quote: "Install glass block windows with vinyl vent.

In your experience what kind of documentation does an auditor want to see to show that specific items of a renovation are under $2,500 and qualify for safe harbor?  

In my profession I am proficient in EXCEL and that is how I do my day-to-day bookkeeping, but is there a more RE specific program, strategy, or template that is useful when it comes to keeping track of RE specific items? 

If all the recent comps were in great condition, had updated kitchens/ bathrooms, granite tops and so on, then you could reasonably expect the value of the subject property to be similar if it also had many of the same characteristics.In regards to specific items, say granite tops or updated bathrooms, you need to think about your target renter.

In my case, my seller wouldn't accept this, or even meet me halfway  however during due diligence I was able to receive a copy of their last U&O inspection report (Which they failed) luckily the report had very specific items to fix, and when I matched that up with my standard inspection report (Who I did through Pillar to Post in Philly) my inspector had more or less caught and called out all of the things in the U&O report. 

Unless it is a very large, specific item you will be hard-pressed to find a contractor that would allow the owner purchase the materials separately.