I'm probably not going to get around to consolidating my Phantom posts from three different blogs but it's not too hard to create an updated index for them. The most recent is from today (and I've already revised it three times) on U.S. Navy Aircraft History: http://thanlont.blogspot.com/2013/03/f4h-1-f4h-1f-f-4a.html
It provides a summary of the F-4A versus F-4B designation change history (in brief, the designation change was related to the change to an uprated J79 engine, not because of the raised canopy as some think) along with an illustration of the differences between the F-4A and F-4B production inlets.
There are several other mentions of the F4H/F-4 on that blog that you can find by typing F4H into the search box on the upper left-hand side of the web page.
The first configuration summary for the early Phantoms is here: http://tailspintopics.blogspot.com/2009/11/early-phantom-iis.html
I followed that up here: http://tailspintopics.blogspot.com/2011/05/early-phantom-iis-redux.html
This is a summary description of the major differences between the F-4A and F-4S: http://tailspintopics.blogspot.com/2012/12/you-cant-tell-phantoms-without-score.html
This post was focused on the stabilator changes over time: http://tailspintopics.blogspot.com/2011/09/f-4-flapstabilizer-change.html
And this one, on the difference between the small and large radomes: http://tailspintopics.blogspot.com/2012/11/f4h-1-large-and-small-radomes.html
This post provided some pictures of the original canopy and was subsequently updated with an illustration of the inlet development history: http://tailhooktopics.blogspot.com/2013/02/f4h-1-flush-canopy.html
Really diving deep, here is an illustrated description of the early RAT: http://tailhooktopics.blogspot.com/2012/12/early-f4h-rat.html
Note that I revisit these posts from time to time and discover reasons to revise them with changes, corrections, and updates. I'm also in the process of refining some of my illustrations of the early F4H changes, so stay tuned.