I think that the biggest issue with your current code is that it is all located in one script. This makes it very hard to read, understand and maintain. A solution to this would be to make your code object-oriented as @unix_system mentioned. This allows you to divide your code into separate classes for every object that is present in your code (a weapon, a bullet, input, et cetera). The biggest advantage of this approach is that you can place every class in a ModuleScript. This way, you can ensure that your code stays under about 100 lines of in every script, which improves maintainability and readability.
You have already done a great job by dividing functionality into functions. Classes are essentially another layer on top of that. Here is a decent tutorial on OOP for ROBLOX: All about Object Oriented Programming.