To add an elaborate on what Bronto says...The engine exhausts are different on an E than a D (GE T-58-10s on Ds, GE-T-58-16s on Es) the Ds with -10s had an oval exhaust while the exhausts on Es with -16s have a 'squarish' appearance.
None of the rotor heads or blades in any of the Academy kits reflect the rotor systems that were installed on As, D, or Fs. They rotor system they do provide for all kits is what was installed after fiberglass blades were introduced with the first E models in 1978-79, So the rotor heads and blades are not accurate for Viet Nam era CH-46s.
The fuel pods on the Academy CH-46E reflects the increased fuel capacity introduced with the later Es. (Early E models had the same fuel capacity as Ds and Fs, but with the increased horsepower of the -16 engines, the range was reduced significantly due to higher fuel consumption rates) and would not be correct for an A or D/F
It has been a while since I last looked at what is in the box on the E as compared ot the D. And I hate to point this out, and I don't mean to sound like a smart a-- but your best starting point to create a D would be to start off with a D...at least with that kit the single biggest problems are the rotor heads and blades...which most people wouldn't catch anyway unless they had spent a bunch of time around Ds, Fs, and Es.
Also, remember to get th direction of rotation of the rotor systems correct, and another problem that some seem to have with these kits is that they show the pilot's and co-pilots escape panels as doors...