I know there is a protective plastic tray that fits over (well under) the brake and fuel lines on the belly of the car. I'll have to remove this when I do my re-line job. Is it best to leave it off and use that stainless steel coil material (link below) on each line as a protective barrier or put the plastic tray back on?

I have been told the plastic tray collects salt and water.

 

I would keep the plastic tray.

Use nicopp brake lines - they won't rust.
And there are 3 steel fuel lines in the tray that need protection.