Quick googling gives flat fee per year for contractors fixing pot holes and that seems like it would be cost saving, but didn't find any info on a per hole system. The fact is that many streets are so badly designed that is not economically feasible to keep them pothole free. They are poorly designed and built because the voters pressured their city leaders to cut costs. So drainage is poor, streets don't get resealed frequently enough if it at all, small cracks are left unfilled, etc. Any given street can be fixed relatively easily, but most of America has more infrastructure than it can afford to maintain. Check out what the American Society of Civil Engineers says about this if you want details. The fact is that a lot of our roads will never pay for themselves in economic benefit even without taking into account maintenance and repairs.
I agree that drivers should actually pay the bulk of the costs for the roads. They should also have to pay fees to pay back all the subsidies they've gotten over the last 100 years to get the infrastructure in place that they are now using. As it is nondrivers subsidize drivers. I am willing to accept that a small portion of road funds should come from general revenue to account for use by emergency services and general economic benefits that accrue. If you don't think drivers should have to pay off all the subsidies then I don't see why mass transit should be forced to compete without subsidies. This is like making special accommodations for a cable provider and helping them pay for new cable being put down and after they are established declare that everything works better with a free market and all new cable providers should compete on merit and price. Also mass transit provides much greater benefit to nonusers than auto travel in that if you remove 10% of peak traffic you reduce congestion and travel times by far more than 10%. Mass transit also exposes nonusers to much less risk than autos do. Mass transit also helps to keep dangerous drivers who know they are dangerous off the roads, saving lives and property. Mass transit also helps people the too poor to own a vehicle to work, reducing drain on other public resources and reducing poverty induced crime. These are all cost savings to nonusers. So if project B improves the value and cuts the cost of project A, it would seem reasonable to that project A share some of its saving with project B.
As for compartmentalizing funds, in addition to not always making sense, I don't think that will help when city leaders feel comfortable lying about what is happening to money. If you had a direct reporting of all money transfers to and from the city, you might be able to see how money is spent but I wouldn't be surprised if they still can obfuscate even if you could get such a report. In any case, compartmentalization or no, there are no consequences for city leaders who spend money in a way the public doesn't like, unless it is so bad and gets so much attention that they get voted out. That is small punishment since they have already benefited and is small consolation to the public that was ripped off, especially since there is no reason to believe a replacement will be more responsible.