1. Even though the recipes exist in JEI, the Distillation Unit does not let me input Crude Oil from either Thermal Series and PneumaticCraft into the Distillation Unit. I have tried inputting a bucket in the GUI, and through pipes from Mekanism and Pipez, but neither work. Only Crude Oil from VE works, both from buckets and pipes.

2. The I/O seems to be very buggy. Even with output set correctly, the machine does not output fluids into other tanks. I have tried pipes from Mekanism and Pipez, and placing tanks from various mods next to the machine.
   
   

The machine will not actively look for tanks to insert fluid to. You'll need to use a mod that can extract from machines via a capability. For example, if you use XNet, you'll have to configure it to extract from the correct side before the fluid can come out of the machine.

There currently is currently no plan to update the machines to directly insert fluids into tanks placed directly next to the machine.

Pipes are now working with #55 on the latest branch. No plans for direct fluid->machine transfer anytime soon.