Or is it simply cosmetic or preventative or an upgrade?

Often times inspectors overlooked them as they are very small and minor but as you can probably already tell, they are extremely important and prevent water intrusion.Your best bet would be to contact a very reputable Siding/roofing contractor and have them go through the entire property and put in the proper drippage flashings seals and caulking necessary and have them insure the work. 

Personally in my experiences we have worked with many Section 8 tenants and we have learned to be able to as you stated screen them a little bit better and root out the good from the bad so that you do have a good experience with a Section 8 tenant.

Will this prevent me from saving for the down payment for the future house?

As others have stated, a well-drafted LLC operating agreement should have language that would prevent management from withholding material facts and/or removal provisions for a manager who doesn't comply.

This prevents Amy confusion about different leases, agreements, etc.

I will definitely screen my buyers more in depth in the future to prevent this from reoccuring. regarding the continued marketing clause, I came up with this to include in my contract. 

Repairs needed, conditon of the property, preventative maintenance needed throughout the year and who will handle4.

Insurance is to prevent loss, not provide profit.  

If you are in a neighborhood with a higher crime rate (C neighborhood), make sure to protect the AC units by putting a cage over them to prevent theft.