The TraceRoute functionality in Workspace Studio will allow you to set the payload for the ICMP packets that are sent. In the application's main settings dialog, choose ICMP, and set the payload to whatever you need. This should cover MTU testing and IDS / firewall.
However, the Toolset's TraceRoute is based on varying the TTL for an ICMP echo request packet, meaning that the TCP port, sequence number, and TCP window size are irrelevant for our particular implementation. Hope this helps.