I have not checked the latest Microcat (Landrover Catalog) but the parts I have listed were valid for 2009 which is well after the last year of the Freeloader 1.
The only theory I have that match the facts your reported and the conjecture on the part number for the tcm and intermediate speed sensor removal is this:
Your vehicle original TCM does not expect/ignores the signal for the intermediate speed sensor even if the pin out are present.
When your vehicle was assembled they took whatever transmission was ready due to something like a stock pile even though it already had intermedia speed sensor knowing the tcm would ignore it.
The new to you tcm expects an intermediate speed sensor and is throwing the code because of it.
The easy way to test this is to swap the tcm to your original one but with your new transmission then clear codes and make sure the battery is disconnected for a good 10 mins.
I am sure this is not what you would want to hear, but in the absence of any more documentation it is the only one I can think of that fit the facts.
The good news is you have everything at hand to test it. Please let me know if you already tested this.