samb has it right. One internal difference (and I have no idea why this was) is that the motor tube is longer and therefore projects further into the main body than the usual 2 3/4 inch long one. As you can see in the pictures, blow-molded nose cone and die-cut fins.
Another difference is that the fin locations are pre-marked on the body tube. Probably a time-saver for a classroom build - no guide to cut out and tape together, then slide on and use to locate marks as per normal Estes practice and no door/drawer jamb needed to extend/connect the lines.
I also see, looking at this example, that the face card image has the balsa nose cone and simple painted on livery. The kit includes the black/red waterslide version of the current blue/red Alpha markings as shown in Marcus' post.
I also just went to the modelrocketbuilding post linked to above, which has another, seemingly later version that the EK-25/1419 that's sitting here next to my iPad as I'm typing this (the one in the just-taken images). My kit has the usual two-RA-2050 rings for centering the motor tube, Chris' kit has the big green single ring that is used in things like the current Generic E2X or SkyWriter. Also, no snap swivels or sandpaper in my kit. Very interesting. I didn't realize there were two Alpha II variants before now - with two different catalog numbers.
Alpha IV was a one-year-only Estes 40th anniversary edition. It's an Alpha III with black fin can and nose cone and a red sort of jeweled-look body tube. Oddly it uses the two-loop plastic launch lug that's found on lots of Estes RTFs rather than a regular one as used on the Alpha III even in its current form.