After the loose or flaking paint is scraped, go ahead and sand the surface. Sanding does two things, it finds more loose paint and removes it plus sanding dulls the surface producing a rougher surface for the primer to grip too. Use a palm sander to speed up the sanding and save your back.
Wash the entire caboose with a mild soap and water. Use a push broom to scrub the surface. A garden hose is fine for rinsing. The washing will remove the dust and pollution, plus any oxidized paint. Allow to dry overnight before proceeding.
The Bulls Eye 123 primer is a good acrylic primer for many surfaces. Go ahead and prime the entire caboose to stabilize the paint that is there. If the "trouble spots" are areas that the acrylic primer can't stick too use Cover Stain, same manufacture, instead.
If you plan on using Sherwin Williams, use either Duration or Super Paint. These paints are their #1 and #2 for quality and stability. Both are 100% acrylic. Also choose a satin or semi-gloss sheen.
When I think caboose I envision a red color. Red is the worst color for stability outside. Plus, it doesn't cover very well, requiring multiple coats. Definitely use the best paint you can afford. A better paint will last longer and look better longer.