Is there anything special I should include in the contract either between me and my partner (I'm planning to include terms of my cash contribution, how we will hold title, who is responsible for what during the rehab and listing, and how disputes will be settled) or us and the seller? 

There is one core factor I am trying to figure out as I found a dispute in view points in these books.

If not how do I dispute that if they proceed?

We are working to bring down the insurance, and we are disputing the tax appraisal so hopefully we can get the margins better.Last year, we added the 4th unit which is costing me $300/mo and renting for $800.  

Keep disputing, might get you a few bucks, but it seems that smoke damage could be cleared in one month.

They will wake up and fix title issues for you, bond around them, or pay you the value of the policy and take title to the property instead of fixing title.There are a lot of "ifs" and "maybes" between here and a resolution that can radically change this answer.  

Currently we are offering to cover 1) drying out of the property, 2) replacement of the damaged floor (includes moving tenants property into storage), 3) 'restoration' - replacing baseboards and drywall removed for drying out.The insurance company is disputing that a) the house was inhabitable during the drying process (note they have removed some of the vinyl floor and b) the final cleaning of the house (the tenant is complaining about dust on the appliances and in the cabinets).I'd like to know how it ended for you.ThanksRob

Guess I have my 2017 resolution now :)

Remember this is very rough and more like bubble diagrams and maybe a rendering or two that are low resolution.

@Ian Tudor the original pics were high resolution...had to change the format.... : )