You seem like you're on the right path, a willingness and awareness to want to learn is usually enough to set you apart from most guys. Even a lot of guys on here - even those who are good at pick up - probably won't dress too well. It won't make your game, but it can certainly help by both making you look good to attract the females and by making you more confident! So keep up the good work! Ok your questions;
1) Your weight and size affects the fit of your clothes - as you seem to have figured out already. When comparing what a skinny guy can wear compared to a heavier guy, in theory you can wear exactly the same things just a few sizes smaller. However, there is also an element of personal taste. For instance, if you know Russell Brand and you like to dress in that sort of skinny jeans, baggy tee shirt style, a skinny guy can pull that off far easier than a bigger guy (even though I'm not a fan of that sort of style on anyone - I'm just using it as an example). Also bear in mind some things like vertical stripes supposedly being slimming whilst horizontal ones may make you look bigger.
The only other point of difference worth bearing in mind is that some skinny guys might make more use of layering than a big muscly guy - layers can help buff you out a bit, whilst muscly guys might wear a skin tight tee shirt and not a lot else to show off their muscles. But that's more of a personal choice thing. Bottom line is you can wear exactly the same as a bigger guy (but in a smaller size) as long as it's something you like and meets all the rules I mentioned in the first post.
2) Yes, I'd agree with both of those. Most 'normal' pants (blue/black/grey jeans and chinos) go with most colours, so you don't need to worry TOO much. Especially if they're dark blue. I'd always go darker as they look more mature as a rule, but if, for example, you've got some stone washed jeans, then you may need to bear in mind the lighter colours on the pants. And if you're wearing coloured chino/shorts or something like those, then you need to be very conscious of what colour the rest of your outfit is.
If you're wearing a tee shirt under a shirt, I'd go with a vneck not a round neck. And yes the colour should be more powerful. But, a note on colour here, if you've got a fairly light complexion and blonde or light brown type hair, then you don't want flourescent type colours. This means that you will need to wear "earthy" colours- as such, the shirt on the outside is almost vertainly going to have to be a neutral colour. if you've got a dark complexion, you can wear brighter clothes more easily and can maybe get away with two brighter colours.
Also, make sure it fits the occasion - maybe a cardigan/wooly type jacket/sports jacket or similar would look better than a shirt, sometimes a shirt on it's own, sometimes a tee on it's own. Don't get stuck wearing one sort of outfit (ie shirt on top of tee shirt) just because one of them looks good.
3) It's a rule that I stick by, but not everyone does. I class shoes alongside accessories as they should complement an outfit rather than be a core piece of it (don't get me wrong - they're still extremely important, possibly THE most important bit, but they should finish the outfit, not be over bearing of it).
I stick to a rule that all of my accessories should match. So I wear brown shoes, a brown belt and a brown watch, for example. The accessories can have more than one colour - but at least one colour must match. A nice touch would be something like this; if you're wearing a polo shirt that has green trim on the sleeves you could wear brown shoes, a brown watch, and a belt that is both brown and green. The brown matches with the accessories and the green matches with the trim. That's an example, but you get the idea. Bottom line though, yes, shoes and belt should match at least to some extent (in my opinion).
And similar colours are usually ok, but sticking with the brown theme, if you've got a very light brown belt and a dark brown (almost black or maybe even ox blood reddy brown) pair of shoes, then they may not have the right effect. Try to keep them within a shade or two of each other if possible.
Get yourself a good looking female wingwoman! Women tend to (massive generalisation that is probably a bit sexist as well, but hey ho!) have a better eye for this stuff than us, so they can help you with that. If she's good looking, then even better