I've configured tomcat server to have multiple server instances, each on a separate port. Here is part on server.xml:
<Server port="8005" shutdown="SHUTDOWN">
...
</Server>
<Server port="8006" shutdown="SHUTDOWN">
...
</Server>
Is it possible to restart only one of them or only some engines in each service?
Defining multiple Server elements in a single server.xml isn't supported. That it works at all is somewhat surprising. You should be using separate Tomcat instances for each of those Server elements.
Once you use separate Tomcat instances, restarting an individual Server is as simple as restarting the instance.
For lower level components (Engine, Host etc.) you can stop/start these via JMX (which you'll need to enable first).