Make them justify that $1,000 if for no other reason than principal and honesty in the relationship...not in an aggressive way, but in a persistently inquisitive one.
Using your figures from before:
Used car: $25,000 @ 3.9% for 60 months = $468 per month
New car: $30,500 @ 0.9% for 60 months = $520 per month
So for an extra $52/month you can get a new, later model car without the "What's been done to this one" worry. I think you mentioned somewhere about putting money down. At 0.9% financing it does not make financial sense, but given today's rates of return, the "perfect" financial decision mostly has impact to the left of the decimal point. A $1,300 down payment would get you below the emotional threshold of $500/month. (Make it $2,000 to give yourself room for error and a $486 payment.)
So...post pics your new car when you get it!!!