Well its really more the things like adding something to an inventory, knowing how to measure where a mouse clicks in 3d space, and things that dont really have a specific answer. Like if you had an inventory, do you use a class? do you use an array list? how do you tell what items are going in an out of your inventory? with a method? a for loop that loops through the inventory? There seem to be multiple solutions to most problems in 3d gaming but I want to learn how to actually apply what ive learned towards a game
In most cases like what you're talking about there's no right and wrong way, there's only different ways. Some are better, some worse, but that analysis depends on the specific needs. We cant help you with that, at least not with the information you've given us. The best thing to do is write your game. You'll learn with experience what works and generally how things fit together, so the next time you do it you will already start off with ideas on how to do these things. But the key is to start small. That way you can finish the game, and finishing is what will give you the experience to do better next time. Quitting or failing usually will only make you more discouraged.
As a more specific answer, and related to "thinking like a programmer", your best option is to do what programmers do for any problem... divide and conquer, simplify, and do general things before you get to the specifics.
For example, you want to make a game with lots of characters, lots of weapons, lots of maps, a bunch of different skills and items that can be picked up, etc. Where to begin? First you make a single map with no characters. Then you put one character in it. Then you give him one weapon. Then you add one pickup item. Then you give him one skill. Then you add multiple skills, then multiple pickups, then multiple weapons, then multiple characters... get the picture? Start with something simple, the add to it. As you add code and features you will naturally need to change it, but that's just how it goes... especially when you're never done it before. Once you'd gone through that several times you'll be able to start writing a new game already taking into account all those things, but for now you dont have the experience. So, think like a programmer, do what I said above and you'll be fine.