Agree with FlyingSquirrel, you can always extend the flatbed if you get rid of the chipper. My chipper has a high feed tray at 36 inches and I've never thought it was a problem, but any higher would start to be.
What I saw on the Morbark's website was 35 to 44 HP. Then they gave two engine types: Kohler and Kubota, (which are probably gas and diesel respectively). Diesel is more expensive and heavier, but seems to bog down much less easily even at the same HP, and brings a disk or drum back to max RPMs faster. I don't think born2cut needs a very powerful chipper if he can dump both chips and logs for 10 bucks a load. Just chip to 4 inches and throw the rest in the trailer? It is about $100 a load out here in Denver and some places charge more if its not all chips.
What exactly do you mean? Extend the flatbed and build a box if I got rid of the chipper? I would agree, Kubota would more than likely be a diesel engine. I've also had Kubota diesels on tractors, many that went 6,000 hours, one even had nearly 10,000 before it started slowing down. The problem is I don't want to go back to diesels. They are great work horses, but god for bid, I've had a few that went sour. When diesels go sour, they'll bend you over backwards. I went to gas trucks, swapped a brand new gas 6.0 in my truck about three weeks ago, $2,500.00 for the engine, and 10 hours putting it in.
As far as chipper size, to be dead honest. We've been renting a 6" for the longest. I've had absolutely zero issues with it. I've ran bigger chippers, but I'm not sure I see the fuss of extra weight, more costly, costlier repairs, less room and so forth; being worth the negatives. Don't let me lie to you, they aren't as efficient as running a 12 or bigger. But I've yet to run across much of our trimmings the 6" wouldn't take. All logs are easily thrown onto the trailer. Dump fee cost us $10.00, no matter if I take a trailer full of logs. But just out of curiosity, aren't logs packed into the tightest form that would could be anyway?
Anyway, I'm looking at these 8" machines. Maybe even a 9" if weight doesn't jump too dramatically. But in all honesty, we've had perfect luck with the 6" machines.