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TCP is problematic to replay/inject due to the hosts maintaining connection state, as you have found.
Google has tools that may or may not solve this if you search for it. Within the tcpreplay suite, there is a utility for this:
https://tcpreplay.appneta.com/wiki/tcpliveplay-man.html
Another solution is to avoid replaying TCP all together and develop a (maybe) simple client or server utility in the programming language of your choice to play the other side of your test.
