There could also be possible extensive termite damage that could have occurred over these years it was vacant.

Use a filing system for all your invoices - physical or electronic.

As long as it's consistent with the lease, you have the right to withhold some of their deposit to cover the damages and cleanup. 

My contractor said he does not want to be in liable for damaging the items during Demo which is fair but I can hire someone to safely remove those items.

Hard to do on 100% financingBig sneaky expenses that sometimes get overlooked are cast iron pipe sewer repair/root damage and older windows.

There's a clause that says it can't be used for physical repairs which makes sense if you have a brick and mortgage store/office but in our case as rental property owners, can I use the loan funds for a repair such as a gutter replacement??? 

I need to break a tenants lease after an incident where the front door was damaged in addition to noise and disruption to the other tenant.

You'll need to check your local laws but I would have treated this as an Abandoned property, I can't take physical possession of the property until the tenant gives me keys or I go through the abandonment process.

I offer to help our tenants, to ensure they're installed correctly - not damaging the frame, or draining improperly.

Many states and municipalities are very strict that security deposits are only to be used for unpaid rent and actual damage to property.