First of all, the class quests are not very visible. My girlfriend just started the game recently, and she didn't notice her story quest until I told her. I'm quite sure she's not the only one.
That's why i would mark the class quests with the (!) marker exactly like sidequests when they get available.
I agree. I think that there should be a visible notification when you rank up that the class quest has become available. Perhaps it should also be mentioned in the tutorials that you may want to check on the guild at different ranks to see if quests have become available, starting at X rank.

I would move the quests (currently at level 20, 30 and 36), to level 10, 18 and 26.

Then I would add another three for each class to expand further on the story of each guild, reaching more epic proportions as the level grows. I'd locate them around level 34, 42 and 50.
I don't see the logic in this. There is no need to have the class quests so close during the early ranks, especially 1-24. The leveling process is so fast as-is that it is more reasonable to set the majority of class quests to the higher end of the scale where leveling takes longer. 20, 25, 30, (34, 38, 42, (44, 46, 48)) sounds like a more reasonable progression.

I would also revamp rewards:
each quest shouldn't give just the guild marks (that at the moment are a bit overabundant anyway), but should award skill points for their specific class (I'm actually of the opinion that every quest and sidequest should *without fail* always reward skill points. Quests being part of the leveling process is now an expected and solidiefied staple of any MMORPG, and people get disappointed and annoyed when they finish a quest witout receiving a reward that contributes to their level progression. Currency is too low-value to be considered worthwile).
I don't agree with this. First of all, when the economy is stagnant currency is not going to be considered worthwhile. This is something they will address, and these are the first steps to stimulate the economy [important]. Secondly, the quests in this game are not considered the same as the quests in any other game. They are not used as a means to progress (even if you can get SP from the mobs). This game is not the same as any other game, even if there are similarities. That should be emphasized. Also, its not hard to make guild marks matter.