Once I finalize my design and proven out the hardware, I will usually build the entire project either on perf board or in some sort of enclosure. I am a hardware guy teaching myself some programming using several different types. I will typically custom build the Arduino compatible hardware only using the necessary parts to support my project. On the software side, I will write and debug many smaller sketches and then create a finished sketch using all of the smaller ones. Like I said earlier, I am a hardware guy and find it easy to just build what I need !!Tom
You are right not to leave it on breadboard, you will have endless problems.You could try strip board https://uk.rs-online.com/mobile/p/stripboards/2065841/ , you can get it like that or with tracks cut or plain. You could go to the next step of learning and get a PCB made.
There are a few construction ideas here that might be interesting for you. (the thread is a bit long but there are lots of ideas discussed). https://forum.arduino.cc/index.php?topic=445951.0