Here's my take on the modal playing stuff- just my understanding and what works for me so someone else may object.
Basically, from a guitarist's perspective keys and note names are more or less irrelevant. Of course they aren't for purposes of communication with other classically trained musicians but for the purposes of soloing and composing all that's relevant is really understanding the interval relationships in terms of numbers and patterns.
When I was about 16 or so and really started to get into music it was actually the Red Hot Chili Peppers that got the ball rolling for me. I saw some live videos of John Frusciante soloing and was just blown away by the fact that he wasn't playing what was recorded on the CD- he was just making it up but it somehow sounded "correct" against the backing music. For some reason, in my passive experience with music I had never noticed this before. I then started on this quest to determine how in the world he was able to do this. It more or less altered the course of my life.
I had some limited understanding from highschool music class about the notion of "scales" or "keys" but didn't really see what relationship they bore to soloing. However, it probably helped a little bit by just allowing me to say, "Ohhh, so that's why that's like that" when I sort of stumbled upon certain relationships on my own.
The first thing I found useful was worldguitar.com which has all of the modes listed and a "jam machine" applet which lets you kind of try them out over a chord progression. Again, I'm not entirely certain how this happened but you start to sort of notice that each of these modes overlap one another and create a kind of network across the entire fretboard of intersecting modes. The beauty of the guitar is of course that it's all relative- once you've got your bearings in the "key" the patterns are always the same.
Eventually when you start to build that muscle memory of the fretboard network of modes, you'll find that as long as you can identify one note that "fits" against what you're listening to your brain and hands will just know where to go. I don't want to be one of those people that just says it magically happens with practice so here are a few little things that helped me to get to that point.
First of all, do your best to always try to "sing out" in your head what you're trying to play- it's very easy to just kind of noodle around in a pentatonic blues scale just going from note to note- it'll sound correct but not necessarily "good". A lot of blues guitarists will often actually sing what they play at the same time while they're performing- if you're able to do this at least in some capacity you'll know it's starting to become second nature. Secondly- always practice in the pitch black. Sounds stupid but it did wonders for me, just key up a track, turn the lights off and try to get your bearings without being able to see anything- it'll really help you get in touch with your "inner musician" hahaha. Thridly, try not to overplay too much. It's easy for us to do this as metal players but you'll find the first component much easier if you just relax and not instinctively play through patterns or arpeggios just for the sake of shredding. Leave space between phrases, really work with strong rhythmic motifs and try to make your guitar act as if it's a voice not a riff machine. Lastly, try to write a lot. This is kind of a two way street- as you start to understand soloing your composition will improve and as you write more and more you'll begin to develop a better understanding of why things are the way they are. Music is a language and the in order to speak it fluently you'll need to both build your vocabulary and understand the grammar and sentence structure.
Most of all what I'm trying to convey is that I think the best way to "learn" this stuff is to learn it in which ever way makes the most sense to you. Again, the communication issue can be a bit of hinderance if you want to be a session player some day but I've always found that it's easier to come at it from a less academic angle. If you've got a good music sense to begin with and some basic understanding of playing guitar you should be able to work through this over the course of a year (or less) if you're really diligent. Then, from there you'll just become more and more fluent in the language of music.
Hope this helps.
EDIT: To explicitly answer the OP's last couple questions- your tunings only matter if you're tuning to something that is not "relatively equivalent" (to make up a term) to standard tuning. So D standard will not change anything for you in terms of the nature of modes, scales or patterns- it will only change the notes names relative to frets, which as far as I'm concerned is meaningless when it comes to actually playing guitar. If however, you change the relationship between any two adjacent strings then you'll shift the modal pattern accordingly. For instance, if you tuned from D standard down to Drop-C, anything you played as you would in standard tuning on the lowest string would have to be shifted
up 2 frets to compensate- this is why power chords on the top strings in dropped tunings are just barred across with one finger while in standard tuning they're played with the index and ring/pinky spread out across two frets. For the purposes of soloing, I find it's best just to avoid that string- haha. I should also add that I do a great deal of composing on keyboards now with digital sound libraries and my non-traditional understanding of music just means I always visualize the keyboard as I would a guitar- that is, in terms of intervals regardless of white and black keys. It doesn't seem to impede my playing at all when writing although I suppose it would present problems in terms of reading music or writing it to a score.
