Using my intercepting application, can I send a tcp request to one of the two applications by filling the Request.EthPacket.Buffer with a new packet that I create and then send it using SendPacketToMstcp or SendPacketToAdapter?
Yes, you can. However, please note that injecting data into the TCP stream is not as easy as it may seem at the first look, because you should properly shift SEQ and ACK fields in your newly inserted packet and all sequent packets.
Would either application be able to tell that the packet didn’t originate from the application it is connected to?
If packet is injected properly then it won’t.