A roof on a typical duplex may cost $8k to tear off and replace.  

I need help deciding if I should keep my primary residence and rent it out or sell it and then move into a new one, I have already done a cash out refi of 60k if we rent it we would get 150-250/ month profit not counting cap ex and if we sold we could get 5k-20k property is worth 250-280 ARV , the property has brand new roof hvac and hardwood floors with in the last year or two we will also be using va loan to buy. ps my wife wants to sell and I want to rent it out 

Even had a brand new roof and young HVAC.

That's where bad experience/nightmare come in.Lastly, to answer your question, to build a basically designed, square/rectangular house without crazy jigsaw puzzled cuts on roof, the following price is a good competitive construction only price for what you need to do:Around $165 per sq ft on conditioned space (for an average 1200 to 1800 sq ft house, 8-9ft high ceiling, everything is investor grade finishes), $90-100 per sq ft for garages/unconditioned storage, $60 per sq ft for porches/opened spaces.  

I had a crazy incident where a huge section of the roof blew off in wind storm in May 2022.

If you buy a package of 6 lesser houses  that means I have 6 roofs, 6 hvac, less cashflow, and likely subpar appreciation(dollar for dollar) compared to better areas.The reduced maintenance costs, higher rents, better tenants, appreciation, and reduced hassle factor for new construction are real and attractive.  

While shopping for a small multi-family building (3 or 4 units), I would like to get an inspection of the building to get an estimate of repair costs if any problems are found (foundation, roof, electrical, plumbing, heating). 

Most people on here think the 3 properties is a horrible way to go but there is a group that goes this way and there is the group that starts off the 9 property way but then stops and focuses on paying them off to be in the little to no debt group and enjoy huge cash flow without as much work and never worry about making a mortgage payment or worrying about having the cash to buy a new roof. 

If the roof needs to be replaced, do you both pay 50% of the cost?

Also, keep in mind that you should have enough profit (NOI minus principal and interest) to be able to realize a reasonable rate of return and still be able to set aside some money for capital expenditures - for example, money for new roofing, paving repairs for drives and parking areas, etc.In the end, you have to get to the other side of analysis though.