I'm just starting out the sentence mining portion of my studies and am really enjoying it so far. however, I have a question which may seem silly. I have many sentences from manga and games I want to use, and I also found reliable english translations.

My question is where do i get the readings for the kanji, considering there are sometimes many choices? Sorry if this question sounds stupid but i seriously don't know how to begin.

http://dic.yahoo.co.jp/ has always worked pretty well for me. You might have to read a few definitions until you get the correct one. ie. 明日 generally isn't pronounced あす, but it can be, depending on the context.

Not that I want to crush your AJATT aspirations or anything... but maybe it's best to start out with a couple thousand basic sentences which have kana and which you can just copy & paste straight into the SRS without having to worry about anything? Then when you get a feel for the language and a decent grasp of vocabulary & grammar you can start to mine sentences directly from games & other sources (I thought all manga had furigana but obviously not).

But if you're determined to start at the deep end, there's always WWJDIC. If you know the English translation, just type in the unconjugated word you need to know the reading for in English (e.g. "eat", not "ate" or "eating") and it'll give you the reading. But going English to Japanese is always risky because of various interpretations of certain words in certain contexts. Like I said, if I were you I'd put games & other media on hold until I had a basic understanding of the language.

You can ask native Japanese speakers on sites like Lang-8 to help you.

My dictionary has most words that involve one or two kanji and show the proper readings for that word. If you get a dictionary you can draw kanji into (or find one on the web, or find out how to do kanji-lookup without drawing them in) then you can find most all of them in a dictionary by looking up that specific word.