I'm not talking about money from Philosophy items, I'm talking about that massive amount of Gil they added to killing the regular monsters in that patch months ago. The potential of that Gil does not drop, ever. Same for Tradecraft Leves, same for Treasure Hunts, same for anything that right out drops Gil (going to laugh if we all get plenty of Platinum Allagan pieces from the new main quests).
Lets take your situation specifically; A Free Company of two people (going to assume two total, not two + you). Smallest plot costs 40M. 3,000Gil per Wanderer's Palace becomes 6,000Gil (not factoring in any Gil from Allagan pieces or Materia). That's around 6666 runs, 30 minutes per run (fairly long run, but who am I to judge) equates to 3333 hours which is around half a year (~140 days);
In 90 days the price of your house will have dropped to 20M, however. If we work off that number, you can actually afford it before the 90 days cause it to halve in price.* The price will reduce a maximum of 360 times in 90 days and will will fall to half its starting price.
This also isn't factoring in the Gil you've already gathered, and again, dungeon farming isn't what I'd consider best, it's just consistent. Really though, I'd say wait for personal housing. Such a small Free Company hardly seems worth it, in my opinion. I'm not against small Free Companies (mine doesn't even have eight full time members), but two people? They have to balance the cost of current housing to all Free Companies, and yours is assuredly an outlier, I'm afraid. There are Free Companies with dozens of members, just apply the same maths to them and they get a house very easily... Knock an 0 off the cost and, well...
I really don't see housing as any different to any other piece of content they're adding. You're not going to be done with Dailies next week. You're not going to finish farming Crystal Tower next week. You're not going to afford a House next week.
All the people saying furniture should be expensive, instead of the plot itself (and using ridiculous single player game analogies), are you not aware of how crafting works in XIV or something? Even if the bloody tables are made from Spruce Lumber, there is no way furniture would ever come close to costing a significant amount. I've got a stack of Spruce Lumber, I don't even need to HQ furniture, it could require ten dozen stacks of Spruce Lumber to build the house and it wouldn't dent my wallet at all... Not that I'd be against them lowering the price somewhat in exchange for basic building materials to set up the house, since that would actually be kind of neat (so far it looks like a house just teleports to your land... wat?), but the amount that would shave off the plot, if SE is committing to this cost, is insignificant.