Replacement Property Must be Same as What Was Identified.

Is there any capital expenditure items (HVAC, Roof) that will need repair / replacement in the next 3-5 years?

I would ask for a $25k roof allowance or ask them to replace the roof now. 

We had a new water service line run 1.5 years ago and replaced the curb trap at that time when everything was exposed.

I can repaint or replace dog damage in a day, next tenants would never know. 

Examples: I take a refundable pet deposit instead of a non-refundable one or a monthly fee, I currently pay the whole water bill without taking money from tenants because the duplex is watered together (I will eventually get a separate meter but the outlay is more than I want to pay right now) assuming it doesn't get out of control, paid for the new doorknobs on the bedrooms because the tenants requested locks despite the lead tenant saying they would pay for it, planning to replace the microwave hood simply because it's louder than it should be though it still works, etc.I'm probably losing out on a minimum of $100 monthly.

Do they all need to be replaced to.

@Jacob PhillipsAt a minimum (beside from your security deposit), you should have cash on hand to replace one of the major mechanical equipment (often the AC/Heater units).   

According to my research the work I am looking to do (replace the tub and surround with a one piece caulk free tile free tub-surround product and replace the vanity) should not take more than a week.

It’s 14 years old and they quoted me $3000 to replace it.