the 3900 is a distant relative of the very same 2.8 our Fiero's came with. It has ALOT of new features, and even though they are the same design, there isn't a part on it that hasn't changed, well, maybe the oil pump drive shaft, but thats where it ends. The new 3900 is an effort to increase the displacment of the longstanding 60º V6 family to improve both horsepower and torque, while still remaining a well tested design that is both efficient and cheep to build. Basically the old pushrod motor is proving that its numbers can be competetive with todays 4 valve DOHC motors, and still be far cheeper and more reliable in both production and maintenence then a DOHC motor, and have better torque and run quieter too. Again its all about the reliability of this particular engine platform. I still wonder when they will make a production aluminum block... That would be sweet. But I don't think that its a reality.
As far as the difference between the 3900 and the 3400 or 3500... The block was modified in a couple really big ways. While the engine still has the 8.818" deck height, the bores center line no longer intersects the center of rotation of the crank, they are now 3mm or about 1/8" lower then that point to make room for the HUGE 99mm bores and the cam, yes about 3.9" thats fricken huge, especially when compared to its origional 89mm 3.5" bore. Still using that 84 MM crank too, however the crank pins are 2.25" and the crank is forged steel 
