When I was growing my first real estate portfolio of small MF properties, I kept a list of non-pressing items that needed to be addressed at the properties.

Current systems and tools:- Assistant to manage payments, invoices, ensure rents come in and chat with tenants for issues- Melio for vendor payments- Baselane for banking - separate accounts for each rental and deposit- Google sheets for Income and Expense reporting- Azibo for rent collection automation with late fee automations- Drive for my leases, SOPs, and documentations of tenants move in/move outGoals of improved system:  ensure I have a read out of how each property is preforming month over month, check on big expense items, ensure vendors get paid, mortgages get paid and rent is coming in, generate APY on float and savings for any big CapEx that comes up, and make my life easier come tax season.Is there a single software people use or what do you do for your business systems to optimize all of this?

literally zero debt and the only negative items on it are some late payments to a CC (just didnt have autopayment on, it's like $23 dings here and there). 

This along with your roof should be one of the 1st items explored. 

The foundational items, roofing, HVAC, plumbing and electrical were newer and needed very minimal replacing and updating.

How are flippers purchasing items such as Tile, LVP, Windows, Doors and so on at an extreme discount?

.- 12/13 the check of course bounces due to her putting a stop payment on the check- 12/13 I was notified that she turned off utilities on 12/12- 12/14 I provided her email stating I would be checking on the property on 12/15 (24 HR notice)- signed lease through August 2018- I have $1650 ($1350 rent and 300 pet deposit) in security deposits- upon checking on property I found that there are no items of value in my property and she had left all keys and garage door openers that I had originally provided her.

Not really sure how much is involved with replacement as some items have seen say there may be asbestos in the duct work.   

However, the LLC will need to chip-in financially to help complete this renovation.My general question is what items should the LLC cover and which should my father cover for best tax benefits?  

I do estimates based on when I think major items will need to be replaced and how much they will cost and how big my portfolio is, etc.