Security Deposit question

[Jennifer Swesen]

First let me say this is my first rental  property. Tenant was there for 3.5 years and always paid on time (last possible day) but I got paid. They moved out almost 2 weeks ago. No keys were left for any doors and locks were replaced while tenant occupied property so I didn't have copies (I know shame on me), shower rod was taken? 2 sets of curtain rods and curtains were taken?    

I asked for items back- response was "had to search to find keys", curtains were ruined when MY basement flooded and ruined them, shower rod was rusty so tenant thought I wouldn't want it, tenant disassembled my curtain rods and would have to find all pieces to get back to me. Tenant contacted me a few days later and said I have everything and I will drop off and told her don't bother everything has been replaced and will come from your security. 

Tenant also moved a dog into property about a year in (200 nonrefundable in lease for pets) and also enclosed an open loft into a bedroom, sheet rocking open space and placing a door on an open entry way. (lease states no construction)  

Tenant asked me if I wanted her to take down the construction and I said no, as I hadn't even seen what it looked like. And quite frankly I was afraid there would end up being a bigger mess left for me. 

So here's my question. Now I am looking at what I should be taking from security deposit. I know new locks and shower and curtain rods and pet security. Can I charge for curtains? Since I told tenant not to remove construction, can I pull from security for that? 

Please help a newbie who is probably too nice to be a landlord.