I'm learning Japanese mainly with books and other "neutral" sources, but I have a female friend who is helping me with that too.
My main concern is if the fact that she being a women can makes me sound weird or funny to native Japanese people.
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Similar to you, I've studied Japanese with various resources, but the majority of the people I've learned conversation from have been women.
On occasion I've been told by someone close to me that I have said things that sound feminine, either in word usage or intonation. I've tried to be careful about that and lately I haven't heard too many complaints in that area. But I may still have a bit of a 'feminine' sound to some of my speech.
From a linguistic point of view, make sure you know what constructions can sound feminine (〜のよ、そうよ、そうだわ, etc.). Just be aware that it is not black or white, some expressions like そうね I think can sound a bit feminine (or not exactly manly), but I've heard normal men say them.
Intonation is more difficult, and watching/listening to a variety of resources (Dramas, movies, podcasts) with male speakers will help. You can try to help your intonation out by practicing speaking lines from various male character, just beware that much of the speech in fictional media (anime, etc.) is exaggerated and doesn't necessarily express the tonality of people in the real world.
I've noticed I tend to pick up the most language from people that I speak with conversationally on a daily basis, so I think it's really good you make friends with one or more Japanese guys. If you can't meet in person, Skype should be fine.
Overall, as long as you have a good balance of male/female speakers in those you speak with the most, I think you will be fine.
Also, if you want to record yourself saying a basic 自己紹介 and upload the MP3 here, maybe some of the native speakers on here can provide feedback about your intonation.
In my experience, sounding similar to the sources that you study from (e.g. textbook, anime, women etc.) is almost like a rite of passage as you learn the language. But as you learn more and more you'll begin to learn the differences in intonation/word choice that fits your particular character, whether it be female or male. For me, this relates similar to English and how you sound when you're a teenager vs. later in life in say, business contexts. You learn that certain words are inappropriate or sound childish and you replace them for their "adult" equivalents. In summing, I wouldn't worry at all, just be extra attentive and experiment and see how native speakers respond to you.