I would drive it all based mainly on skill challenges, at least for something like a stronghold where the character has land, peasants, whatever that they can manage. Let them simply execute a fairly straightforward skill challenge every so often, say whenever they want to do something with their stronghold or something significant happens with it, or every year if nothing else. This will just basically determine how well the character carried out whatever lordly function was involved.
I would grade success:
Dismal failure - You have a serious problem. The peasants are revolting, the new tower you just built was faulty and collapsed, etc. Either you can live with the problem, throw gold at it, or fix it yourself. Depending on what you were attempting to accomplish this could be time for the DM to introduce a plot hook.
Failure - OK, things aren't going as well as could be expected. Maybe the local estates aren't so well managed and lost some money, etc. Some money could be thrown at the problem, or you can live with it (maybe you can't afford proper castle maintenance this year, the DM can determine what exactly this entails).
Success - Things are fine. The place pays for itself, everyone is happy, the new tower is all spiffy and there were no problems raising money to build it, etc.
Acquiring such a place doesn't involve money. It involves skill challenges and/or other DM provided means. Skill challenges and RP would let you say convince the local King to let you build a castle in an unsettled area, find pioneers willing to help build it and found a village, etc. The point is, money isn't likely to be a big factor. You promise some peasants some land, they work for you. You get the land from the King to start with, etc. If you want some extra spiffy special features, then you have to say get the dwarves to agree to send over a few of their guys to build those for you (and of course they need a favor done in return). If the PCs WANT to substitute money for some part of this, by all means let them, it is their choice.
The same process should work for smaller establishments as long as they would be expected to be self sustaining. A farm, thief's guild, temple, etc would fall into that category. A wizard could build a tower and sell his services or teach, etc. If the thing doesn't have any means of support, or the PCs aren't willing to RP dealing with that, then there can still be options for acquisition that are cash neutral. Inheritance, grant, seizure, etc. The trick then is upkeep. How do you rationalize that? If its not a big place, then just don't worry about it. A 2k gp house on the edge of town might cost the character 50 or 100 gp a year to keep up. Its like bar tabs, just don't worry about it.