download optifine (search it on google) and edit the glass textures in the ctm.png, then when you are done, just drag it into the main folder for your texture pack where terrain.png and pack.png, etc. are.
It's gray to start, but minecraft will color it based on the color in grasscolor.png in the misc folder. If you put color into it, minecraft will keep the color you add and simply change the gray parts.
On your Minecraft launcher screen, there should be a button titled "Options." Click that, and click "Force Update" then "OK" and then log in to Minecraft. Wait for it to load, and it should work. If not, I don't know what's wrong.
I might, if you give me specifics on what you are looking for. (example: I want torches to be... etc.) or something along those lines. (You don't have to do every block with that either, but it would be helpful.) Also on the mobs I need specifics.
I don't know if this is out of your coding abilities or not, but maybe some pistons that extend farther than normal ones? These would be helpful for things like doors. Also, maybe some transparent blocks so that the players of the map would not see it but would still collide with it. This would be helpful if you wanted to keep people in a certain area but let them see the outside or whatever. If these are too hard, don't bother doing it. I wouldn't even know how to start coding this!
I suggest looking up a tutorial on YouTube. That is what got me started. There is a pretty good (but outdated, though the method still works) tutorial by RandomMacFive.