If I had rear ended someone in July and no police report was filed or insurance claim can he contact me 3 months later and tell me I owe him $1000 for repairs? And there were a few scratches which he told me were from prior accidents?

Can he contact you? I suspect he already has.

You can obviously challenge him in court -- it'll probably be your word against his.

Yes, and he may sue you if you don't settle with them.

And depending on the "scratches" 1000 is not that bad, I had a very minor that hit my bumper and it was over 700.