First of all, thanks RR. And John, you beat me to it. IIRC, Miscanthus is 15 to 20 times less energy dense (by volume) than coal. So that would give you one train every 4 minutes at the 100MG/year ethanol plant! Maybe pyrolysis of biomass locally into bio-oil is worth looking at? (producing bio-oil, syngas and heat) And then ship the oil to more centralized bio-refineries?

So the plants must be small, co located with the material and using a source that can be harvested easily year round.

Or some plant which processes the biomass to a transportable form must be.

There are some candidates for transportable forms.  Torrefaction can be used to dry and densify biomass, make its properties more uniform and reduce the dry mass by about 30% while losing only about 10% of the energy; the product is better than coal in some ways because it is not hygroscopic.  Torrefied biomass can be gasified more easily than raw biomass because it is both dry and friable.  There is also fast pyrolysis to bio-oil.

Farmers use 5 billion gallons of diesel per year today.

At 140,000 BTU/gal, that's about 0.7 quads.

Herbacious biomass is about 15 million BTU per bone-dry ton.  If 70% of the energy can be produced as storable fuel, that's 10.5 million BTU/ton.  0.7 quads of fuel would require about 67 million tons of biomass.  The USA has a potential of about 300 million tons of crop wastes alone (straw, corn stover, etc.); we can power agricultural machinery from the farm, it's everything else that we need to worry about.

I didn't look at the details of Coskata's technology, but in general I am not so pessimistic about the feasibility of 2nd generation (= cellulosic) biomass conversion - even in the colder climate of Germany. This applies especially to of producing bio-gas using fermenters - a widespread and mature technology that farmers use to produce heat and / or electricity. With some more recent technologies (e.g. using extruders), that allegedly result in a positive EROEI, the applicability of the fermenters is enhanced to celullosic matter that could hardly be used before, e.g. wooden twigs.
About two years ago a study of the renowned Leipzig Institute for Energy assessed that this way on the long run this could supply the entire natural gas demand of Germany.
Electicity produced in these can already be fed into the national electricity network (and is paid by a feed in tariff) and feeding in the gas in to the national gas pipeline network probably will be possible from 2014.
At the time of the study biogas was still more expensive than natgas (I should look up the exact price tag), but with the present import prices it is certainly more than competitive.
According to this study (and others) using small, decentral fermenters feeding into the gas pipeline network avoids the need of transporting low-energy biomass over long distances. This is also an advantage over other more complex biofuel technologies developed by Choren or (with a somewhat less centralized approach) Lurgi.
Until recently biofuels as car fuel additive had a strong political support (possibly also due to agriculture lobbyism). But with increasing evidences of the ecological and technical limits of (1st generation) biofuel is now aiming lower. However I fear that due to our strong car lobby it will still take a while until there is a clear target to concentrate on developing the much more efficient electricity for transportation and conserve hydrocarbons for applications where they cannot be replaced.