I work at the RR on the intermodal side, where all the trucks meet rail.  I can say this area has done nothing but explode and it's not stopping.  Long haul trucking is dead.  You can't even find the truckers who are willing to perform it if the $$ as right.  I talk to trucking companies all day about their business.  There going to be fine so long as people keep swallowing fuel surcharges that increase in some cases weekly.  

It seems to have lulled now though, but even many executives at these co's know that the future is rail.  They realize that it is simply more efficient to move distances on rail and move trucking back to strict local.  The funny thing is when I approach the topic of diesel prices and question changes made to personal habits etc and many just don't see the WHOLE forest.

I've heard thru a credible source that manufacturers of large diesel trucks will be tacking up to 10,000 dollars extra for 2007 emission requirement trucks for the fire service. If the fire service has to pay so much extra then I assume long haulers will be as well when they go to buy new trucks.
I don't really know what you're talking about.  Many trucking co's are middlemen and nothing more.  Most truckers are private contractors free to move to anther company for whatever the reason.  I run into issues with truckers damaged our equip but moved to another company and we can't charge people only companies.  So if they will be forced to take on $10K in charges, it will get passed on somehow.  Long haul trucking is dying if it's not dead already.  
I am not sure of the amount, but you are correct that there are additional costs associated with purchasing a new diesel vehicle.

The change consists of additional particulate traps, catalytic converters, etc... got a few friends that work in the heavy truck sector emmissions... it's all they talk about

The next step after intermodal is for businesses to start getting rail sidings installed like in Days of Yore. We'll see how long that takes.
Many businesses still have these.  I worked in a factory for two years in my first few years of college and there was a section of the plant where we stored rail cars still on the tracks.  We used the rail cars for storage ironically.  I don't think it would take much to reactivate these hook ups throughout the country.  I'm sure I'll see companies going back to this in my lifetime.