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.

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.

Some slight progress

The engraving on the candlestick:

If the engraving is reversed we get "unus postulo tantum vos", which according to Google Translate is Latin for "You only need one".

The last undeciphered message:

I did a letter frequency analysis of the message and the frequency fits well with normal English. This suggests that the letters themselves are not ciphered, just their order is rearranged.

Is anyone else working on this?

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.

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.