Personally, from your post I can't understand what you are doing.
But here is my opinion and what I do anyway.
What I do is use heisig for writing (Which is what it's for) and then use the "Kanji in context" books to learn how to read.
The general process of most people who do heisig is:
-Learn how to write with RTK 1
(And if your like me, RTK 3 as well for an extra ~1,000 kanji... Just for the fun of it)
-Go through Tae Kim's site for grammar
-Use a book like "Kanji in Context" or "Kanji odyssey" to learn how to read.
Some people (Including myself) change the heisig keywords to Japanese keywords:
wrightak - After Remembering the Kanji Volume 1
The important thing about this is that you stop relying on English keywords, a lot of which don't actually give the correct meaning to the kanji... they are only a handle to remember the writing after all.
I mean, why he chose the keyword "Town" for 村 and "Village" for 町 I don't know, but most people seem to swap these around anyway.
(I did because it just got on my nerves)
The reason for learning to read through sentences is because for the majority of people (It seems) learning how to read kanji in sentences is the best and most efficient way.
Eventually you end up being able to guess readings (Unless it happens to be an irregular one, but you learn those on a need to know basis anyway)
And lets face it, you may as well learn how to read kanji in context anyway, since this is how you will be reading them forever.
The best place to ask questions about heisig related stuff really is:
Reviewing the Kanji - Learning Japanese
Everybody over there has either completed heisig, is thinking about starting it, or is in progress. (Which also means that threads don't turn into heisig flame wars lol)
Lots of ideas are always thrown around when it comes to SRS and a lot of people will probably have far better answers than I on this subject
Anyway, my opinion:
-Don't take the keywords as actual meanings (If this is what you are doing)
-Learn to read by reading
