IMHO, I wouldn't have the whole thing set around one ship... Have a coupla missions on the Iceni, a couple on miscellaneous other ships with objectives like disable the sub-space drive or board the craft and take the command centre.
Although it would be a good idea to have the storyline running parralel to the original, it is also a good idea for it to have its own, individual storyline

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"Supernova, ya supernova, supernova goes pop
supernova, ya think it's over but the supernova don't stop" PM5K
Death:"Arnold Judas Rimmer... your life is over. You will travel with me to the-"
#knees death in the groin#
Rimmer:"Remember matey, it's only the good that die young"
Kudoth, god of pointless educational programs.