Hello, How are you? I think that you have a problem with extra components, let's start to explain it to you:
1. You have three bipolar stepper motors that are powered by L298N from 5 to 12 VDC with a maximum current of 2A each, which adds up to 6A in total.
2. The L298N can power 2 stepper motors at the same time, but I note that you may need them to work separately. So we are not going to change that.
3. The LM2596 gives you 5VDC with a maximum current of 3A. (I don't know what component your power on that)
4. The XL4015 gives you 5VDC with a maximum current of 5A. (I don't know what component your power on that)
5. In the 5V and 9V DC stages gives you fluctuations due to the same reason that you have with the circuit since begin.
6. The source that you have gives you a maximum current of 4A and the stepper motors need 6A or 7A, That is solved with a source from 8A or 10A. With that, it goes away the fluctuations in these stages.
In addition, it is possible that you have some extra components and everything could work better for you with fewer components.
Sorry, I forgot show you my credentials I am Electronic Engineer and Electronic Technician, I got more than 10 years of working with PCB. I usually use Proteus, Kicad, and more to make my Bakelite designs. Because in the field of electronics it uses a lot. Also, I have many experiences working with different kinds of microprocessors such as stm32, ESP8266, Arduino, PIC, etc.