One thing I simply dont understand in T4 is that John Connor seems to have no idea what a T-800 looks like, is made from, et al. Yet in every other way he seems to have the experiences of the JC from other films. What gives?
I don't follow. In the beginning of the film there's a whole scene centered around Connor recognizing the schematic of a T-800 under development years earlier than expected on the Skynet facility's computer, with the nameless redshirt saying "that's the one you told us about" or something. There's no indication that he doesn't recognize T-800s in the film.
If you're talking about him not recognizing Marcus however, that's because Marcus was something he'd never encountered before; a metal endoskeleton built over and connected to existing human internal organs rather than simply human skin coated over a metal endoskeleton like the T-800.