From what I remember the 3-valve engine has two intake and a single exhaust allowing the cylinder to fill with air faster (and less resistance). Basically it breathes better. On the pickups the 3V engines also came with better headers (good enough that 3V engines really didn't benefit that much from aftermarket headers as the stock ones are really good).
I had a 1999 F-250 with a 2V and a 2008 F-350 with the 3V and the difference in HP, torque, etc. was very noticeable between the two.
Looking at the sales the E-Series sold about 100k-125k a year..not to shabby:
Ford E-Series Sales Figures - GOOD CAR BAD CAR
Looks like Ford is the commercial van leader, even after the introduction of the Transit (wow!):
GOOD CAR BAD CAR: Van Sales
Interesting, here is just about everything you'll ever want to know about the Vans and stripped chassis vehicles:
https://www.fleet.ford.com/truckbbas...-17-14-v46.pdf
(Take a look at the cutaway image on page 25!)