Help connecting custom ATMega328PB using serial FTDI
In such a case, start with a working setup and then work your way step-by-step to your final setup. Like:


Start with 5V, 16 MHz, existing bootloader, Arduino IDE with 'hello world' sketch.
Change to 3.3V (lab supply) and 8 MHz. verify (baudrate will be halved)
use your FTDI-to-serial circuit. verify.
change to your 3.3V supply. verify.
change to using your IDE and ISP. verify.


If the step that causes things to beak is still to big, divide it into smaller steps. Divide and conquer! This is the same technique I use to find out what causes a compiler to crash on a 30k lines application. Takes some time, but you'll get there in the end.