Here's a simple enough notion:
Resources is a Standing - it's about your place in society, not how much you have. So let's rename it market - it's more about your connections in that specific area, which makes it the sales and acquisitions variation upon Influence. Use Resources, then, to be more about tracking purchasing power. When you make a Market roll, and fail, you lose a die and the amount of Resources it will take to get what you want is increased. I'd suggest, in this method, that Resources should still be on a similar track, and especially large scores, like stealing an atium cache, might instead become plot items - because otherwise, they're really the end of such a campaign anyways. And trying to track boxings and clippings directly would be REALLY unfair to Coinshots. If the team gets to Resources 10 (keeping in mind that they had to spend some Resources on the job they just ran), it's time to consider changing the narrative a bit because at that point they're set.
As for the loss of items with Long Breathers, is there really any reason not to completely ignore that for anything that isn't incriminating? IE, you need to ditch your disguises, sure, because it''s a problem should anyone find them. But that doesn't mean you have to get rid of your new dueling cane that you got to help sell your cover. You can also redefine the length of a Long Breather (you may not like DnD, but that's basically the number on fix for pacing issues raised by 4th's Short/Extended Rest mechanic).
And if you think that you don't have an array of villains to work with with just the gangs, noble houses, and TLR, consider Shadowrun. You have the Corporate Court at the top - the Lord Ruler. Then the Megacorps - so, let's say that there's division and infighting in the Steel Ministry, and the different factions are your Megacorps. The actual direct governing body of a city/dominance/whatever is the government - powerful there, but not beyond their borders and still having to answer to the CC/TRL. Nobles not directly in charge, then, become analogous to the international criminal organizations that are a fixture to Shadowrun (you really ought to stay off their radar), and the Skaa gangs to the street level gangs (get out of their city, or even to a more affluent part of that city, and your safe - and you can play them against each other; they can still be a pretty serious threat if you're in their territory). They're only as homogeneous as you let them be.
All that said, I'm seeing a lot of "I write"... What about the rest of the table? This is a collaborative game, they're writing the story too. You don't put the story in front of them and see what they do - you come up with a job, or some task that must be faced. The story evolves out of how they choose to approach it, the Complications you choose to add, the interaction between their Heroes and your Villains, and how they respond to the Turning Points involved - and in the case of players with characters of high Spirit, the editing they choose to do (perfect for instituting heist tropes). In fact, try a different structure. Rather than trying to encapsulate everything into one single session, let them do some planning OUTSIDE of the session - either by laying out the next target before the session ends, or by putting that up online (Google Docs would work wonderfully for this purpose, and lets them plan things out together). Try to get your head wrapped a little bit more around the collaborative concept - it has a way of drawing people in more, too.