Hi, welcome to the forum.You connected a 9V battery directly ? How ? Perhaps you damaged something ? Can you test how much of your components is still working ?Which transmitter is that ? How is it connected ? The cheap 433MHz transmitters (with round saw based oscillator) work at 5V, and maybe a little at 4V, but maybe not so good at 3V. A battery powered ATmega chip is often used with three AA batteries or a Li-ion or Lipo cell.I prefer to have VCC-GND decoupling with 100nF capacitor, I don't care about a 10uF.Can you tell more ? Which ATmega chip ? Internal 8MHz or external crystal ? Which bootloader ?
It should work. Your barebone at 5V should almost be the same as the Arduino Uno.Can you make a photo of it ? So we can see the wiring.
An AVR running on the internal 8 MHz clock doesn't need the 22 pF caps for a 16 MHz crystal.The 2 CLK pins are open, I think it's PortB that has all 8 bits usable.You can run 3.3V at 8 MHz. You can wire 3.3V devices directly, many devices, microSD adapters.If you want to go from 9V or 12V to less, efficiently, look up buck converters including make your own.And then look at boost converters, you can run on a 1.8V source.