Q: Should I bother learning the meanings of individual kanji? If yes, how should I go about it?

A: Learning the meanings of individual kanji is essential, but this should be done in the context of words and preferably also sentences. If I were studying kanji now, I would start by learning the basic kanji meaning(s) through the KLC mnemonic, then write it out several times while thinking about the mnemonic, then go through its vocab trying to grok the meaning of the kanji and how it works in building words, then read the Graded Reading Sets exercises for that kanji, twice, being sure to cover the phonetic and English glosses while doing so. After every 5 or 10 kanji, I would test myself on the meanings of those kanji, and read through their GRS exercises once more.

Q: Should I try to memorize kanji readings?

A: While it is important to familiarize yourself with a kanji’s readings from the beginning, you should not trouble yourself to memorize them. Instead, after studying a kanji in the KLC, practice reading it using its set of exercises in the KLC Graded Reading Sets. This will give you plenty of chances to learn its basic readings and usages in a realistic context, especially since it will appear in the exercises of kanji that follow it in the sequence. I think you will find that approach more effective, in several ways, than trying to memorize kanji readings in isolation.

Q: Which KLC vocabulary words should I study, and how should I study them?

A: Prior to creating the Graded Reading Sets, I recommended learners to memorize the example words marked with superscript circles in the KLC, presumably using flash cards. But I believe such rote memorization has been largely obviated by the GRS, which allow learners to master each kanji’s most vital example words through repeated exposure in meaningful context. The sheer quantity of GRS material suggests to me that those who read and re-read each volume will have little need to memorize KLC vocabulary as a separate task.

I do recommend that you (a) pay close attention to the target-kanji words within each reading set, (b) understand how they are being used, and (c) re-read each set before too long (perhaps reviewing after every 5 or 10 sets).

You will come across some KLC vocabulary that do not appear in any of the GRS exercises. Creating the GRS was a learning process, and after about kanji 500 or so I realized I should try to make sure the KLC vocabulary items were represented. Even before that I did have a system in place to increase the probability that KLC vocab would be represented, but in the first few GRS volumes you’re more likely to find some unrepresented vocabulary.

Q: Can I use the GRS as a standalone resource without using the Kodansha KLC?

A: The Graded Reading Sets are best used with the KLC, but several people have mentioned that they are using the GRS even though they had already learned the kanji by another method. Apparently they like the structured reading practice with the English translations and grammar support. As long as you know most of the kanji introduced up to the point where you’re using it, the GRS can be a very useful stand-alone resource without the KLC.

Q: I’ve reached the halfway mark in the KLC and I would like to start reading some authentic materials. Is there any reading material you would recommend I start with?

A: If I were in your shoes, I might go through the list of Original Works at the end of the Graded Reading Sets books and see if there’s something of interest personally. Perhaps there’s something you have already read, which will make it easier for you to follow the Japanese? You can download parallel texts for those from whatever source is listed in the Sources section, e.g, Aozora Bunko.

I personally love the translation for Crito. The text is short and the translation is delightfully casual. You could read through the English in minutes, and then try your hand at the Japanese.
Japanese: http://e-freetext.net/critoj.html
English: Google it

For a parallel-text paperback, I recommend Exploring Japanese Literature by Giles Murray.

Besides literature, my favorite reading for learning foreign languages is reading news sites and current affairs blogs. By definition, these give you something new to come back for every day or every week. Armed with some background knowledge and a mouseover J-E word lookup browser plugin like Yomichan, it’s possible to make headway even with only 1000 kanji or so.

ABOVE ALL, I suggest jumping into material that is relevant to you personally and professionally—this is the reading that will be most useful and meaningful to you, and which you’ll be best positioned to understand.

Q: Which kanji am I most likely to run across before I’ve reached them in the KLC sequence? 

A: As explained in the Introduction to the KLC, each kanji’s frequency of use was balanced with several other important factors in determining its place in the learning sequence. For this reason, there are a few kanji in the second half that you are likely to see quite a bit before you reach them in the KLC sequence. You may want to skip ahead to preview these eight in particular (asterisked items mainly for reading literature or subtitles):
1358僕*, 1407君*, 1475 達*, 1583 残, 1681 題, 1715 深, 1970 離, 2155 誰*

Of all the kanji in the KLC sequence, these eight show up latest in relation to their frequency, if one includes literature and subtitles.

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