If you look at the manual which is in specifications on this site you will see the improvements the manufacturers have incorporated into these trucks in the technical information manual pages.They have already made a lot of the improvements you aim to achieve but as manufacturers they are limited by emission regulations and safety regs. They have done a reasonable job improving engine perforrmance and economy, suspension, steering and braking ability to mention just a few.
You have to drive one to appreciate the differnce cos its quite a sharp contrast.
Although I have not been restricted by warranty limitations for over 2 years and am free to do whatever I like to the vehicle I cant really see any point in altering the engine in any way, why would I want to drive a 2ton truck at over 120mph?
I will make a few changes to it would like to do a lift and better wheels and tyres at some stage but am in no hurry to do that for the time being.
I would like the opportunity to use a veg conversion but am hoping the hydro kit might be a possibility for the common rail engine as it seems a possible way to improve economy, it will be an interesting item to dabble with. Whatever I do I will keep the truck for a while yet and look towards replacing it with the next new model depending what they come up with and providing they change the engine block which is well past its sell-by date.
Looking forward to seeing the improvements you are making Yoda, its a huge achievement rebuilding the engine and fitting a veg system, I hope all goes well and the water injection is really interesting if it can be achieved, definitely will gain a cleaner engine as a bonus.