Which way round for the master cylinders?

The standard Rush brake pack comes with two master cylinders of different sizes: 5/8" and 3/4". Most people end up with the smaller one connected to the front brakes. However, it's worth asking Peter at DJ what to do. You should also follow the instructions in the build manual with respect to balancing the brakes carefully. If you can't get the brakes right following that procedure then you might like to try swapping the master cylinders around. Remember that the smaller cylinder gives more braking effort when connected to the same brakes.

Why won't the oil filter fit?

If you find your oil filter wants to go where the chassis is, then you'll probably need to fit a remote filter mounting. Think Automotive sell these, and appear on the links page.