WOW.. 40k plus deposits on a home to be built.. ??? 

You can't charge extra pet rent or even a pet deposit because it's legally not considered a pet.

You’re not using a PM, AND you’re assuming you can charge a service animal a deposit and pet rent?

  $2500 deposit is put down. 

Key points include:Security Deposits: In Indiana, there’s no legal cap on security deposits, but you must return the deposit (minus any valid deductions) within 45 days of the tenant vacating the property.Evictions: Follow the formal process carefully.

We also received a $2400 security deposit.

I just had tenants move out of my investment property (duplex) without paying for the last month's rent, and the damage they inflicted onto the property exceeds their security deposit amount.

The law does NOT apply to landlords:With less then 5 rental unitsThat live in one unit of a duplex and rent out the other unitThat rent out rooms in the home they occupySo, landlords can no longer state in their rental ads, "Section 8 not accepted".The reverse is also true, "Section 8 only", cannot be used.We've always recommended screening S8 tenants the same way as cash-paying tenants.Landlords waiving application fees and/or security deposits only for S8 prospects may also be violating Fair Housing.

No free weeks, no reduced deposit, etc.

Nothing you mention is "ordinary" and you should charge for all of it. dodged a bullet there thats a very good price take it from the security deposit and call yourself lucky.