Some partial results.
The deciphered message:
If the numbers after the message are seen as ASCII characters we get "tHe KeY iS tHe tHiRD PRiMe COUntRY OF LASt". I don't immediately see any new clue in whether capitals are used or not.
The first undeciphered message:
Some fiddling with letter substitutions changes "Qrpqsia… Qdr irxq sp n psgkfr orvropnf" into "Testing... The next is a simple reversal".
The second undeciphered message:
Using A = Z, B = Y, etc, this message becomes
To the Commander of Blood: Thank you for the test message. I assume that was what you shall use to decode. At any rate, we know that Vixen knows...and that given conditions, he would immediately report it to the other side. To send back, do the same thing as this time.
To Wolf Fencer 3: I can't say much here, there may be spies. But wait for another message; I'll expLIAn eveRything.
The messages on the flag at the back:
A = 1 etc, gives "BLITZEN VIXEN"
The message on the flag over the doors;
A = 1 and Rot13 gives "DONNER CAROL"
A possible clue from Rudolph's diary:
The capital letters give: "IDOTNINIETIIR". If one ignores the I's and the T's, we get "DONNER".
I suspect the big clue is the last undeciphered message, though I haven't cracked it yet:
It is wriiten in words of $5$ letters (except the last words) and $5$ is the third prime number. Probably a connection there.
