Rust in hollow areas of engine hatch?

I am restoring a Kombi and starting to work on the engine hatch - it has some hollow sections that have some surface-type rust inside (some I can see but I just know it is there throughout)

What is the best way to deal with this - the hatch is off the van

Do I wash it out with rust convertor, water and metho?

Do I then try to get some paint in there, or do I wait until the outside is painted and spray some fishoil?

I don't want to ignore it and find that the lid rusts out in a year or two

any thoughts?