Hey rdodd,
The answer = Yes/No/Maybe.
I am unsure of your knowledge of the inner workings of the VE injection pump, so I don't know exactly how to answer this. I am no Robert Bosch, but I have spent many hours dissecting several types of VE pumps, as well as dyno tuning, and a lot of reading in Bosch manuals to see what makes these things tick. Basically, anything that is done to the pump to increase its output will add more "stress" to the cam plate and rollers. In order for the pump to move more fuel, the control collar must be moved farther rearward to allow for less fuel to be emptied out of the spill port. When there is more fuel being pushed out to the injectors, there is pressure for a longer period of time on the cam plate and rollers. The amount of pressure will remain the same because of the consistant unseating pressure of the delivery valves and pop-off pressure of the injectors.
Chances are if you ask a technician at an injection pump shop about tuning a VE, they will probably tell you that tampering with it will significantly reduce its life. But, I have been told that I cant do something by the experts, or that it wont work, when it really does. I believe there are a few of us here that have done a little tampering, and have had thousands of trouble free miles (over 55,000 miles for me). What happens is that the hard surface becomes worn, and it will flake off. If a worn pump is really turned up the wear process can become quite rapid causing pump failure. Another form of pump wear is between the plunger and barrel. This is due to the hours/rpm of service. Increasing the amount of fuel doesn't really play a role here.
Being a variable displacement pump, no additional stress is added if no additional fuel is moved. So if the "extra" power is not used there will be no more wear than with stock settings. On the other hand, if the extra power is always used, then chances are the rate of wear will also increase. The amount of stress that is added by modifying the AFC is relatively minimal.
One thing that can be done to relieve some of the stress on the pump is to install larger injectors. The higher flow rate of the larger injectors make the pumps job a little easier. So, by adding large injectors and installing a modified AFC pin the pump may actually not have to work as hard as with stock parts, while improving drive ability.
Another thing that can be done to increase the service life of the pump is to treat the fuel - its lubrication. Over the years the amount of sulfur allowed in diesel has reduced, and will likely continue to. The sulfur in the fuel helps lubricate. This means that there is greater potential for wear. So, periodically adding a good lubricant to the fuel will help prolong the life of the pump and injectors.
Mike