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.

Is there a specific item that is causing the low value?

What about warranties for specific items like appliances, or outside water mains? 

My question is, I have invoices for what those specific items cost so do I still have to have a professional cost segregation done to break them out of straight line depreciation.

Are there specific items to be aware of? 

Obviously there will be some state specific items but any good lawyer will know that too.

If they have more expensive possessions or need riders for specific items (one guy had a few high end musical instruments) it can end up higher.Speaking as someone that had his place broken into by 'friends' while young and renting, I wish I'd have had a renter's policy.