Don't go with the plastic bed liner - it'll just scratch the heck out of the new paint and finish. Bikes don't put a lot of wear and tear on the bed - its the other junk you end up taking with you. I would just be careful and not worry about a liner.
If the bed is totally metal - not wood and metal strips, maybe spray some extra sealer over it so it is more resistant.
If this is a rod and not a classic - I'd recommend a sprayed in liner, like Rhinolinning - these can be color matched (to some extent) and work really well.
