My first question would be did you do a pre-move out inpsection? In CA the landlord is required to offer a pre-move out inspection within 2 weeks of move out date. At that time we notate all repairs needed with an estimate of cost of repairs. That provides a tenant the opportunity to find a licensed contractor who may be able to do the repairs cheaper. How this would apply to you is you would know what the landlord intended to charge you for.
I guess this is not nation-wide, but the standard in CA is paint should last 3 years. If a tenant lives in apt. more than 3 years no charge for painting. Between 2-3 years then 33% cost of paint. 1-2 years then 66% cost of paint. Less than 1 year 100%. The question is if touch up walls included the water damage areas.
As a property manager who conducts and sets rates tenants will pay on moveout after inspections, I have to say the cleaning seems fair. Most tenants want to clean and get all their deposit back. But the questione comes down to: Is it really rent ready? Most tenants do a good job with obvious areas, but did they take the blinds down and clean the top and each slat? Same with ceiling fan blades and all the hard to get areas. Did they remove stove top and clean around burners, get all grease off range hood. Might be tough for you to dispute cleaning.
Bulbs...that's a tough one. I never charged for bulbs because it seems like going too far. But the standard is an outgoing tenant is suppose to leave unit in same condition as when they moved in with the exception of normal wear and tear. So if they can prove bulbs were new when you moved in, then they can charge for burned out bulbs at move out.
Clog for sink $25...that's cheap. We can't find a plumber that won't charge at least $40 just to drive out to the property and they they charge for the repair on top of that. Here's the test for a clog...fill the sink up with water and pull the drain. If you get the whirlpool as water drains out, then water is being sucked through the drain and no clog. If a plumber snaked the drain, then they likely will say on the bill...found hair or whatever they pulled out. So the pm should be able to prove why they are charging for that.
While they don't seem to be cutting you any slack on move out expenses, it doesn't seem they are going overboard either. You're doing the right thing to dispute with the pm company before going to court. It's my experience if a tenant howls loud and long enough and they were reasonable good tenants, we would let items go that might be difficult to prove like switch plate, light bulbs, burner pans (surprised they're charging for that as they almost always have burn marks).
One thing that stands out is they did not make the proper effort to repair the roof. Obviously, they can't work in the rain. Once the rain stops, they can do proper repairs. Since you had repeated issues, I would raise hell about how that interfered with and interrupted your ability to live a normal life. Since water ran down side of wall what they likely did is plugged a hole enough that it re-routed the water. So, your argument is there should be some trade off...your having to deal with leaks for striking several of the lesser items they are charging you for. Most owners/pms will be reasonable and make the trade to avoid the time/expense of going to court.
Good luck and let us know how you meeting goes.