In Indiana a landlord has 45 days to return a security deposit to a departing tenant. It is not unusual that even after a final walk through further damage above normal wear and tear may be found. Pet damage as in offensive odors would fall in the category of damage. This is especially true if pets accidentally urinated (or sprayed) on carpet; such odors would sink into carpets and padding underneath and could go as deep as into the subfloors. Carpet cleaning would only address the top carpet and would temporarily mask the odor. Often the only option is to remove the carpet and padding (and sometimes treat the floors underneath). Sounds like your landlord attempted the least expensive way first (carpet cleaning) but that didn't work and the only other option was carpet replacement.
Carpet replacement in a rental is typically prorated over a 10 year life.
If you disagree with the amount kept from your security deposit you typically write what is known as a "demand" letter, demanding what you believe you are fairly owed and giving the landlord a certain amount of time (say, two weeks) to return these funds to you. If no satisfaction then your next option is to consider filing a lawsuit for these funds.
It's nice that you put in a new shower curtain rod, a shelf track in a fridge that you broke, a toilet seat and some paint but these things play no role in the issue above. It's unfortunate the dryer didn't work for the last 3-4 weeks but not having a dryer does not make house uninhabitable and it's a bit late to throw this into the mix by asking for a credit on rent in a place you no longer reside in.
Stop trying to toss everything you think you now deserve into this business and focus on the fact that any cost of carpet replacement from your pet damaging this carpet should only be charged to you as determined by the prorated cost of the original carpet.
Gail

