Have you tried opening the edited save in pkhex after exporting it to check if the changes are seen by it? Did you make sure to click save in the items window?
For gen 1 and 2 you can use pikasav. For gen 3 you can use a-save by kazowar. For gen 4 and 5 you can use pokegen by codr. All of which are available in the downloads section. If you want to edit more than pokemon and items I don't think their is anything public to do so except a mystery gift injector for gen 3.