Hi, It's me again. My suggestion, remove plesk, since both eprints and koha on your system, are designed to work with apache, and both can co-existed as virtualhost on apache without much of problem. Plesk is really good if you need to provide webhosting (mainly wordpress+roundcube/horde webmail+imap+postfix) and such web apps. But since it use nginx as frontend and put apache in the back caused problem with apps such as koha and eprints that expect apache at the frontend. I know this because I tried to install both plesk+koha+eprints on the same system already. It success at "some" level, but mostly the problem was I don't familiar with koha, and eprints. Also, in this case eventhough you install plesk with koha+eprints, plesk itself didn't provide anything that you can access to config or koha or eprint, unlike those vhost/wordpress/roundcube that its installed by itself. If you expect that plesk will gave you some ways to manage koha and eprints, no it didn't.
Also, since, you have already running these system on VPS already, I'd suggest you to install koha, eprints on different VPS, by itself. It possibly to make them on the same system, but from koha wiki, koha itself need a lot of resource. From my installation just plain koha, no other library resources, no user, (except admin) it comsume 800MB of memory. So for busy library, it will need more resource later. You don't want to share resource of koha system with other. I'm not sure about eprints.