I am looking at a rehab in the hood and it does not have a furnace or any duct work.

And with tenants, you know it'll go unchecked.If you can reroute the duct using smooth-walled fittings, I would move the exhaust port along the wall several feet, either horizontally or vertically and secure the ductwork to the wall using metal straps.

With new paint, it shouldn't be the walls.Clean the ductwork as far as you can reach and then blow an ozone generator down them.The insides of all your cabinets need to be scrubbed, unless they were painted.Just cleaning the carpets won't do it, if the smoke got down into the carpet padding.Probably, all the window coverings need to be replaced, not just cleaned.It may be something else.

We have also seen cats and other animals tear into the ac duct work and make a nice air conditioned house for themselves and their litter.

I have cleaned out eviction units, filed court papers, been threatened by tenants, cleaned ductwork, replaced faucets and power outlets, ceiling fans , woken up at 1am dealing with drunk tenants on the phone etc etc etc.When I confronted him last night he made the statement that "one unit has had no trouble/I've had to spend no time there" which is true --but other units have consumed MORE time so it evens out--as long as I am paid.

So with that extended intro aside, the house has electric baseboard heat with no existing ductwork.

You should make sure that "return" ductwork gets included, and not just "supply" ductwork.

This is to remove old boiler, radiators, install duct work, and install a furnace and ac unit.

Just some random thoughts to be condsidered...The AC filter is installed on the return side of the ductwork, just before the air handler.

I would then negotiate from that point a profit split with 50% being the absolute highest and worst case for YOU.As to HVAC system new for 1200 sq. ft, a 3 or 3.5 ton is more than sufficient and you can get that done for approx $6k, although it can depend on electrical modifications necessary, electric panel upgrades, gas lines, and ductwork materials.If you are in So CAL, I can get you a good HVAC contractor.