Al,
Sorry to hear what's been happening to you. Starting off, which dealer sold this to you? I'd love to warn others so that they don't buy from them.
Secondly, having a Whipple Supercharger on a 6.5 NA engine has happened. It's not very common, but it does exist.
My recommendation in regards to motor removal would be to purchase a service manual for the truck. They come on CD's, and can be purchased from a variety of places. The cheapest I've found is
http://www.bluehummer.com.
The motor comes out from the top/front. You do need to tear apart parts of the interior to access necessary stuff.
As for what may have happened - your Whippled supercharged engine produces a good chunk of power, but you also have to watch something called the Exhaust Gas Temp. If you don't watch the EGT, you will crack the block. When that happens, you can throw a connecting rod and have all sorts of other problems. Water pump issues can occur as well.
The reason for this is due to the fact that non-turbo 6.5L diesels have a higher compression ratio, which means that monitoring engine vitals become critial.
As for tearing into the engine - that's going to be normal. Every 10k miles, the oil for the Whipple needs to be changed. You'll also have to monitor and check for head gasket leaks and watch your injector pump to ensure that it's not delivering too much fuel. Every once in a while, you'll also have to have your engine checked for piston cracks.
This is mainly due to having the supercharger. It gives you good performance, but it does have it's own support headaches.
Hope this helps,
Steve