I am unclear on a couple of items I have been discussing with a fellow RE investor.  

It was itemized and the majority of the list was for things that were marked as ok on the checkout list. e.g. blinds ok, then charged $20 for new blinds, exhaust fans o.k., then charged for new exhaust fans, etc.

If it's an older property, though, you really need to know the age and lifespan of the bigger CAPEX items. 

You'll need to know those items before you can come up with a good game plan to move forward.

And in general, what other items do you recommend I look at.

The landlord has 21 days to send you a itemized damage list and the remaining deposit.

Make sure you aren't in a rent controlled area or that your tenant is not section 8.Enforce items in the agreement that you've been lax on.

I am not sure if there is any more downside to any of the items you already listed.

Given the roof and maintenance issues, you may not want to rush into these without thorough due diligence just to save on taxes - capital items could potentially eat away any tax savings.  

They are issuing title insurance on the property, but I dont see how you can insure the title without those 2 items.