While I am not as experienced in programming as yourself, I would recommend creating a GDD (Game Design Document) first. This is not a 20 minute project as you may spend several hours or days on it.

By writing down all of your ideas and concepts, to include details such as sounds, music, graphics you want to do, features of your game, skills that characters will use, settings, world maps/dungeons, and so on, you can have a clear idea of the project in front of you.

Once this is complete, you have a road map to your entire project. Of course you can change things as you go along, but the framework is laid. At this point, you can now pick a reasonable spot to begin, such as developing the character and their skills, perhaps the progression system. For this, I'll leave it up to you and the advice of a more experience programmer in RPGs.

However, as you begin, you can simply work from this GDD, and you will be able to "check off" things that you've completed and work in some sort of linear fashion, making sure you aren't forgetting anything and capturing all the content you want.

Cheers. (I have a template of a GDD if you're interested)

If you want to just get done with it, have you considered using a game engine to avoid this work and be able to get directly to the point?

If you intend on actually making the engine, I would believe that having created another engine before you have already went through some of the stones on the path. So this would be a little easier, even tho, once you reach unseen territory it'll be a new experience.

Anyway, I would start from the basics, how do I want to do maps? Using simple tiles? Ok, so you create a simple tile based map with an integer matrix representing textures. Simple map done? Now on to the drawable objects, such as the controllable character. A simple character placed on a location on the map. Now, how does he move? What are his animations? How do I work on the animations for the character sprites?

Great, now you have a base character that you can use to build enemies and npcs, being able to separate the npc behavior and enemy behavior in different entities, now that the components that all characters (player controlled, enemies, npcs, everything) have, are already done.

Long story short, what I'm trying to say is, I would take steps during which you would be able to see the progress and test fast. This is the way I build everything. Being able to actually make the minimum viable product fast will allow you to actually test how things work, find things you didn't expect when you planned, find gameplay issues, etc.

Making a design document can be a good thing if you have a billion ideas and you want have a great idea of how you want your game to be on the long run, but in my opinion considering the actual development, doing small steps one at a time and being able to see things working will give you better results overall.

And in the end, planning game design will not help you in writing clear code. Perhaps you should invest your time in improving your development knowledge, learning a bit more about development patterns, since the problems you face seem to be regarding code itself.