It is a top/bottom style duplex with a flat roof and a basement so there should be no issues around ducting. each floor is around 1,100 sq ft  Any idea how much I should be looking to get this quoted for?  

Water heater, roof, electrical panel?

It depends on the age, construction, roof style, etc.

Like, you can't pay over $45k and make a decent profit(15-20%) kind of work - foundation issues, new roof, new siding, new bathrooms, new kitchen, etc etc etc.

The house is a 1971 block, slab on grade with truss hip roof with an L shaped footprint. 

They should own, renovate, and manage the property all under one roof.

Up/down double $57,000 purchase price (hopefully less)PITI = approx $500/mo with 25% down conventional loan$14,250 down + closing costscurrent rents total just over $1200/mo for both - leases in placelandlord currently pays about $200/mo for water/sewer/trashI figure about 10% vacancy and 10% maintenance which leaves me with about $400 monthly cash flowThe two major concerns I have are that it needs a new roof (tear-off) and that it has a funky layout.

The roof was re-done prior to me buying the place which I knew but being young and naive and didn't realize what else needed to be replaced. 

Up/down double $57,000 purchase price (hopefully less)PITI = approx $500/mo with 25% down conventional loan$14,250 down + closing costscurrent rents total just over $1200/mo for both - leases in placelandlord currently pays about $200/mo for water/sewer/trashI figure about 10% vacancy and 10% maintenance which leaves me with about $400 monthly cash flowThe two major concerns I have are that it needs a new roof (tear-off) and that it has a funky layout.

Roofs, vehicles, furnace, etc are each depreciated on their own schedule as defined by the IRS.