Question:  How do you handle transportation for in-stream placement of large wood with the root wads still attached?  The two operators I have dealt with have said the root wads have to be cut off, which takes away the anchoring and complexity value of the large wood. 

Options

Low-boy trailer: rather than a standard log hauling trailer. The main concern that the truckers have is that their hydraulic hoses will get entangled in the roots and damaged. You will probably have to cut off the back end of the piece, so probably the bottom 40 - 50 ft would remain. The tops can be transported separately and plugged in under the piece with the root wad.

Excavator: rather than a standard log loader to get the boles and root wads on the trailer. Alternately, some low boys have winches that could pull them onto the trailer if they can be pushed/dragged close to the end of the trailer. We've used an excavator to unload the bole/root wads, and have also used a cable yarding system to place them where excavators cannot reach.

Large flat-bed truck or Chunk box:  It's a large trailer with high sides that is able to get the root wad in the box and not interfere with traffic.  Move the large wood in the evening when traffic is not as heavy.

Self loader:  to transport whole trees (with roots).  (Locally) they charge about $100/hour (includes truck + pilot car for oversize load).  We have found some operators reluctant to do it so we have just kept looking until we found someone willing.  Clean the rocks and dirt out of the roots and then to wrap them really well with plastic silt fence to prevent rocks from falling into people's windshields.