The remainder of the security deposit will be issued to me as credits towards the repair of the big items - cabinets, flooring, bathtub cracks etc.

At one point I could hear them in the walls, under the floor, and underneath the bathtub. 

My wife says that we need to redo the bathroom and but in a bath tub because any perspective tenants with young kids will not rent our property without a tub.

She said the tenant had a slow draining bathtub and rather then call her they tried to fix it themselves.

Inside the house the toilets and bathtub have yellow water.

Cleaning charges the apt should be left as clean as you received it or you'll expect to be charged for cleaning.. wear and tear isn't leaving the bathtub with 2 years of built up soap scum, or the toilet never cleaned out.. or the oven with burnt on crud left in the bottom, or crayon marks on walls ect....What's normal wear and tear well it's average use. 

Probably 2 long, parallel onesBathroom 7000Replace flooring with LVP (waterproof kind), if vanity can be saved - save, sand and paint, replace counter top with manufactured quartz, replace sink, replace plumbing, replace faucet, replace lighting, replace bathtub with new fiberglass bathtub and tiles around the shower area (builder grade)Flooring @ 2 a sqftSave if possible, clean, if damaged, replace.

I'm sure your plans are finalized, and i'd ask realtors (and the wifey) their opinion, but I'd try hard to get a bathtub on the first floor.

But oftentimes it is dry in there and they can just March right in, swim through the P trap water and pop up in the bathtub,  Sinks,  Toilets or floor drains.

Reglazed bathtub and surround, installed new premade vanities.