Who holds the 3rd private key? I assume some kind of an escrow ?
You need 2 out of 3 keys signing the transaction. So if the seller refuses to sign the transaction, you need the 3rd key holder to sign it (escrow?).
Does anybody know a software which could make advanced transaction with custom inputs and outputs, and sign it
A lot of tools can do that.
But this won't help you at all since you'd need the private keys to sign the transaction (which you don't have).
You have 2 options. Either (1) get the seller to sign the transaction or (2) get the 3rd keyholder to sign the transaction.