You need vitasdk.
make the payload
Copy fat.bin to installer/res
CMake the installer mkdir build && cd build && cmake .. && make
Firmware specific offsets are in first.c and nsbl.h. Logo is raw framebuffer data gzipped. If you make this too big (bigger than original logo size), you WILL perma-brick your Vita.
The source is for advanced users only. Users should download the prebuilt package, Henkaku Enso. If something goes wrong, you WILL perma-brick your Vita. There is no recovery, even if you have a hardware mod. The only possible recovery is if you have a hardware mod and you dump the eMMC before getting bricked, then you can restore the dump. Dumps are device-specific and encrypted with a device-specific key.
Again, even if you just change the logo, there's a good chance you will perma-brick your Vita. You have been warned.