The brake lines and fuel lines run along the side of the rail that the factory floor rests on. With the new pan in place, the lines need to be rerouted and remounted.
Handy tip: If ever you have to do this, disconnect the clutch line at the master cylinder at the start. Getting the brake line out without moving the clutch line can be done, but not without bending up the brake line.
I reused the upper half of the brake line, and bent a new section with a union to join the two just in front of the new floor section.
This is the new rear section:
Handy tip: clamp the end of the brake line you are shaping so that it can't rotate away from you while you are trying to bend it. I used the brake flaring tool you can see in the background of the photo above to hold the end.
I flattened out and reversed the factory line holder brackets so that they could be mounted to the side of the new pan. I may use a spacer and reverse these at some point so that they are retained against the side of the tunnel (or lecky ties will be added).
Pathway of the new brake line at the rear of the pan: