You can put rubber trim molding in the space between the top skin and side panel. This will clean it up and prevent light from escaping through the seam.
The top hole was used for a pricer or advertisement banner. A round piece went down through the hole into the casting inside. Most people (including me) just plug them or fill them. A 3/4" solid metal grommet works great.-Steve
Well I decided to space the top up slightly with shims and that seemed to work. I noticed the picture you show of the hole plug on the unrestored pump seems to have a rubber gasket between the top and side panel. I'll wait to see if much light escapes before deciding if that is needed. Thanks for the info on the hole plug as well.