There really isn't any order that you need to go in to get all the combinations but there are five sets of two numbers. [It may be worth noting that each piece of the combination will tell you where it should fit in the final combination. I.e., the "First" combination listed below is not the first two digits of the combination.]
The order of the combination has been changed recently. The guide has been updated to reflect the changes. as of 2-7-2011
First combination: Go to the top [Sixth] floor there will be a room description in the southeastern room that indicates there's a platinum ushabit. "Pull ush" will open a secret CPK room up(The work room), inside there will be a hidden long description desk, take all desk. If nothings there, check it again later. (scribbled note)
Second combination: You will need a bell boy's uniform and hat, found on the NPC's running around, go to the fifth floor there will be a locked southeast door. Wearing the bell boy's uniform (level 115) and cap knock on the door. When someone answers say room service. Kill Pynai for another part of the puzzle, most likely have to do multiple times. (a sheet of pink stationery)
Third combination: Buy a key from the front desk you will receive an imp, this acts like a magic mirror and when someone says something its repeated at the front desk. Drop this imp in the room with the sidhe shaman, 2nd floor, wait around at the front desk until you overhear a conversation containing the set of numbers. The conversation seems to occur about every Alyrian hour or so.
If you happen to be in the room when the shaman is supposed to meet with the psionic, this will happen:
A sidhe psionic peers at you as if he is trying to see into the very depths of your soul. A sidhe psionic says, 'I think I'll come back later.' A sidhe psionic returns whence he came. A sidhe psionic wanders in to the room.
If they've already met, the shaman will have an official missive from General Hesieno in his inventory.
Fourth combination: This one comes from an ethereal NPC that is located in all east and two south from the front desk. You must pick up a piece of blowfish from the cart- should be one east from front desk. Drop that in the room with the ethereal mob, she will eat it and die shortly after. Like all of the other parts you will probably need to do this multiple times. (sheet of paper)
Fifth combination: Check the safe on the 3rd floor, the key that you bought earlier. It's in a SW room with a painting on the wall, you will need to search for the safe, hopefully you bought some +search as its difficult to find, the truffles from Minx in Rune are a great help. If there's a note there grab it, if not check this part later. (sealed letter)
After you have all five sets of numbers, go to the front desk, and turn the numbers in the above order by doing 'pull [number]' then 'pull lock' to open the north and receive the mark. It seems like if you enter ~5 wrong combinations, the security system will kick in and not let you enter any more for some period of time.
After opening the door you may optionally fight a captive phoenix.
As of 3/7/11 anyone standing in room formed with person who unlocks is also granted mark (worked with form of 4, all 4 received mark).