Anyway security deposits are to repair damage caused by the tenant not to repair routine wear and tear items.  

Should I call out the damaged items during the walk through?

Junk yards typically have battery acid leaks, motor oil leaks, gasoline spills and other items relating to electronics.

This budget works depending on the area you are looking.If you don't like how your agent is performing, then get another one, but ask yourself are you being realistic in your search (An example would be looking for a duplex in Northern Liberties, or Point breeze with your budget and all your wish list items checked.

I called several lenders and one was 75% LTV, one was extremely slow so I pulled the application, and another was 80% (who I went with).The refinanced property had everything practically new (wiring, plumbing, kitchens, bathrooms, decks, etc.) with few items less than 5 years old (roof, siding, furnaces/AC), but the windows were 10 years old. 

This is one of those major items to double check for when calculating repairs and making an offer. 

With the Trulias, Zillows, etc. out there they can capture interested buyers for the area.

The logic being it'll be difficult to raise rents or get them to move out.Also, I feel unsure whether I've accurately captured all the property's expenses.

If your looking at a syndicated fund there are some definite items to keep in mind.

I recommend educating yourself by utilizing all of the free knowledge that is floating around on this site just waiting to be captured.