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The fist step in preventing collisions within your network would be to remove all hubs; they are simply a source of problems and nothing more.
When a frame enters a hub it will exit out all ports, creating unnecessary traffic on your network; whereas a switch will only send the frame out of the correct port -- where the destination machine resides. All ports on a hub belong to the same collision domain; conversely, on a switch each port belongs to one collision domain.
In many cases, I've seen problematic hubs generate garbage traffic that would affect most workstations and servers on the network, so keep away from them.
Secondly, you've got around 120 ports available on your network, which is a fairly large amount for one flat network. I usually start to break networks with more than 50 hosts into smaller segments in order to avoid broadcast/collision problems.
It might be a good idea to look into breaking the network into smaller pieces, using widely known Virtual Local Area Networks (VLANs). With VLANs, you effectively create smaller, separate networks and join them using either a router or Layer 3 switch.
If you're interested in learning more about VLANs and how you can connect them between each other, you can visit my firewall.cx website, where the topic is analyzed extensively.
You also mentioned that you wanted to remove the DNS server from your primary server. Depending on your network setup, this might not be a good idea, especially if you're running Microsoft Active Directory which requires the DNS service in order to function correctly.
However, if you've got a workgroup, then moving the DNS server to a different machine shouldn't be that much of a problem.
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