since you had been running the minecraft server as root in the minecraft users home directory there will be a bunch of old root owned files in the minecraft users home directory. I think the best thing to do here is (as root) is delete all those root owned files (in the minecraft users directory) and then, don't do things as root.
You can see how owns various files and directories by using ls with the -l flag. Ie
Alternatively you can change the ownership of those files using the chown command.
chown minecraft.minecraft install.sh.1
Again this would have to be done as root if the file install.sh.1 is owned by root.
PS. I'm glad you appreciate my help, but it would be great if you could click on the "Did you find this post helpful? Yes" links. ;-)