Joined: Dec 2013
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Heisig added, removed, rearranged, and otherwise made edits to the book with every edition (this being the purpose of new editions, after all). You should regard the final edition (6th) as what Heisig believes to be the best collection of characters for a single book. If you would like to study additional kanji, you could always download the RTK 6th Ed. Anki deck and see which kanji do not match what you already have.
However, I think it's being a bit pedantic to worry so much about the minor details of added/removed kanji in Heisig's books. Heisig gives you a tool-set which should enable you to easily conquer any new kanji you see on your own. Those kanji he added or removed will turn up eventually, and you can study them on an as-needed basis. It's not about completing a collection, it's about familiarizing yourself with the kanji and preparing for future learning: a few dozen missed kanji won't make any difference, I promise.
Edited: 2014-03-25, 6:35 pm
Joined: Jul 2010
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Well you have to keep in mind before 2010 the jouyou were 1945, not 2042. So the answer to your question first question is that Heisig already had included future jouyou in RTK before 2010, and so the 2220 kanji of the 6th edition include all the jouyou and more.
In the search tab, search for the word "supplement" in thread titles, and you'll find threads where the kanji supplement (to the 5th edition) is described. You'll have to add them by hand to the site though you might find lists in those threads.
As for the readings, I think only 23 of the new jouyou weren't in the old RTK1+3, so you'll find all the others readings in your old editions of RTK2 and RTK3. For those 23 you'll have to look elsewhere (latest edition of RTK2, online, ...).
And I don't think it's pedantic to want precise, reliable information, especially when it's the Japanese government that recommends you know this information.
Edited: 2014-03-25, 7:11 pm