I'd start with handymen (we've run across a few that were way more talented and versatile than I realized) to knock out as much of the little stuff as I could (painting, tiling, light electrical and plumbing, cabinet/countertop replacement, knocking down and putting up walls, etc.). 

It depends on the configuration but I had all the plumbing redone in the basement along with a water filtration system (brown stinky water too!). 

Ensure your HVAC and Roof are solid, check the plumbing etc. 

I, and a couple of other investors that I know, have worked with MainLine Plumbing & Drain for projects and inspections similar to what you're looking to do I believe.2-oh-six, 294 9691, I've worked with both Rick and Jim.

In other words, if you respond to needing a handyman, a painter, light electrical or plumbing worker on Craigslist, you're bound to get the same guy!  

I was just inside one of my units fixing some plumbing, and I noticed they had taken down 3 smoke alarms and the only carbon monoxide alarm.  

Include estimates for each type of work--roof, rough carpentry, finish carpentry, plumbing, electrical, flooring, wall covering, mold remediation, etc.

Plus, cost sharing on capital expenses like new roof, plumbing, etc. in the future seems to be desirable with the uncertainty of the economy.

As to the rest, I have seen having to spend 20% more than expected as we had foundation problems that we did not expect and also real bad plumbing behind the walls.  

The major rehab items included: new roof, plumbing, electrical, wall and flooring repairs, water damage repair from leaking plumbing, etc.