On a side note, KY requires you keep their deposits seperate, and disclose the bank account number where the funds reside.

Since this can add up quickly, from a legal standpoint am I making my LLC protections vulnerable by regularly depositing personal funds to the LLC checking account?

I come along and put a Purchase Agreement together with the seller and give them a deposit.

But typical thinking is, if the carpet was damaged by the tenants dogs then you would not be repairing normally and the deposit can be used to return the property back to it's original condition. 

I think if you terminate the lease before the least is up, then you need to refund the full deposit and pay all moving cost and give the tenant a little spending money.Joe Gore

For example, I often see Buyers purchase property thinking there is a $1,000 deposit but then the tenant claims it was $2,000 because they paid the last month's rent.

All our tenants are month to month, and we get first, last and a security deposit prior to move in so that helps set the tone.

Consider all the things that could go wrong and see if the lease addresses them: unauthorized pets or tenants, early termination, security deposit, lease violations, late rent, eviction, lawn maintenance, parking, etc.5.

In the past I have asked for a higher deposit but I just dont want to deal with any potential non payment issues nor evictions. 

If you are paying in cash, you'd have the bank write a letter indicating you have the capital on deposit or you can also print out your bank statement showing the funds.