Yes, it can be done. And CANBUS, NMEA2000 and J1939 is a boating project. Boats have engines.
So Despair not, today there are really cool kits (even ones that can add EFI and J1939 to a Chrysler L engine (318, 360) or big block that NEVER HAD J1939).
If you don't want to design your own, buy a pro-tuner kit. You might consider a Diesel performance bolt on (chip) kit for engine controllers.
http://www.comfleet.com/pages/Pittsburgh_Power.html et al. You need to know what type of diesel the tuning kit can use. One of many
http://store.edelbrock.com/dieselperformancesystems-2.aspx Get a diesel protuner magazine. See
http://www.tuningbox.com/ (ad inifinitem). And more ...
http://www.idc-solutions.net/MackE-7DieselPerformance.html Spend the time to research this and ask around. Don't do whatever the first shop says, get a second opinion. Read up on it.
Finally there is the switch and resistor trick accross the EGR sensors. Fools the ECM. But as Doug said you should not do this.

There are so many options it's unbelievable.
You generally program all of these these with a laptop or a hand held.
-------------------------------------------- or Build it your self -----------------------------------
To understand CANBUS, you'd want to get the set of J1939 SAE message docs from the SAE site. About $599. Don't buy it unless you have to. Go a friends shop and borrow it.
Getting the Electronics Lab together is not cheap, but it's worth it. Once you have the skills, you can kick A** over the NMEA 2000 installers and other guys.
Stage the learning....
First. since you've never used a microcontroller, get some skills (Order servo and Nuts and Volts Magazine, and buy a simple microcontroller kit). Build something with it. Easiest is the Parallax Basic Stamp (Radio Shack). This gets you some basic skills. A better choice is an e-blocks kit. You need an CANBUS reader for the PC (KVASER Leaf Light).
http://microcontrollershop.com/product_info.php?products_id=2363Second - DO A Listener Project : Other than the Basic Stamp which is a throwaway project that takes a day, you need to pick a good CANBUS learning evaluation board. (LIke the Luminary 8962). If you cannot program C, use a Flowcode development kit. like
http://www.cancapture.com/cancapture/functionblocks.html etc. You are going to build a listener project. You might be $800 into the project Mikroe makes some good options.
Third, since this is a talker you need to select and develop the talker and the tuning curve for the EGR. You have to understand how how will it respond to the sensor messages? Also you can "s*rew things up" with a talker that sends incorrect messages while you are debugging. I would be comfortable with debugging that, but would guess few others are.
I therefore suggest a pro-tuner kit (or going to a protuner shop). Ask them what makes sense for your needs.
Anyway. I would build it if I had the time. But I am an MS in Comp Sci, and an engineer.
Unzinced ships sink at slips.