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Will the choice of chapter colors I use to paint my minis affect my options for gameplay? such as not having access to special characters or units?

I'm confused about the major/minor drawbacks section in the codex for SM...

As you can tell I'm very new to this.

I think you may have the old codex, the current one does not have the advantages/drawbacks system.

But in answer to your question your choice of colour scheme does not matter for characters, just paint them in your scheme and put them in your list.

So it basically comes down to "well this guy isn't actually part of my army, but within the context of our gaming table..."?

Is it the same for weapons (IE units with plasmaguns have to actually have plasmaguns)?

Colours dont matter, you could have bright pink CSM and they would be the same as a pro painted thousand sons colour scheme. As for weapons it depends who you are playing, some people are all about WYSIWYG (what you see is what you get). If your just playing with friends it doesn't matter. I've even used Khorne beserkers as Ork Kommandos in friendlys simply because I couldnt afford kommandos at the time. As long as everyone knows whats up, it shouldnt be a big deal.

Great! thanks guys! I have the AOBR starter kit plus another tac squad that i bought about 2 years ago, but the hobby never stuck. I'm looking to get back into it, and I'm getting some supplies. If you could take a look at this list I drew up and tell me if it's a good idea, that would be awesome. In return I promise to post pics once I start painting them

http://pastebin.com/YLVuewTL

I might get two of those brushes if they are good... don't want to pay for more shipping later.

on a supply front it might be easier to buy as much of it from one place, Games workshop will sell all the paints you want and I find their quality good, glue you will be better off going to a hobby store and buying it there (Games workshop glue is terrible).

A quick run down to get started is

your required paints (including washes, base colours, ect)

a few brushes, one larger , one medium and one small

plastic cement (plastic glue)

super glue (for resin/metal/finecast models.

a water tub (for paint water)

a good place to paint (an old desk is good or put a protective sheet on a table)

light source (small lamp (helps with seeing what you are doing))

a sharp hobby knife (Stanley knife or exacto knife)

a file (a nail file will work fine)

this is a good start and most will be cheap or allready avaliable like the light and the water pot, any questions feel free to PM me and I will also check this thread too

hope this helps