Building a Bike for the First Time

Hello,
I am planning on building a bike from the frame up for the first time. After some research, I've decided I want to build an endurance road bike for under $1000. I found that I need the following components:

• Frame
• Wheels
• Headset
• Saddle
• Chainset
• Cassette
• Handlebars
• Shifters
• Crankset
• Breaks-thinking of getting mechanical disc breaks.
• Tons of tools

I'm a little confused though (if you couldn't already tell). It seems like there are several ways to go about this. I could either get all the components separately and call the manufacturer/consult the seller's website to make sure each part is compatible with the others, or I could just buy a frameset and a "gruppo"/groupset. I'm not really sure which I should be doing. I'm leaning towards just buying a groupset since I'm sure there are many things I'm missing in my list above, but at the same time, I feel like it would be more fun to get each part separately so I can really understand what is going on, which is part of my motivation for building a bike in the first place. Could someone please give me some tips or point me in the right direction for this project. I'm also not sure what type of tools I should be buying and what brand I should be buying from at my price point. Sorry for so many questions, it just feels like I've been searching in the dark about this for the last few days. Any help would be appreciated. Thanks a lot!