I would like to connect these 2 boards together. Left one has male header, right one female. Ground and 3V3 supply are not pin-to-pin aligned, while all other pins are. What would be the best way to connect these two boards together (besides nasty individual jumper wires or custom PCB between these two)?
Create a wiring harness using the proper mating connectors for each side. You can then route any pin on the first connector to any pin on the second connector.
Here are some connectors that would probably work...
XG5M-5035-N, 25 pin x 2 row, 0.1" pitch, female, $5.83 on Digikey
Personally, I would add this header to the male connector only for the matching pins and not for your 3.3V volts supply and ground pins. Then, you could use those nasty jumpers for 3.3V and ground pins. This would elevate your connections and allow you to have some room to wire power and ground accordingly.