Is there a counterparty whitepaper? What about a specification?
The link you provided seems dead by now but there is an online documentation available at http://counterparty.io/docs/about_counterparty/.
There is a counterparty whitepaper: https://github.com/CounterpartyXCP/Counterparty
Go to https://github.com/CounterpartyXCP/Documentation/ and search the repo for "protocol specification" (or API or whatever). The current link for the protocol specification is https://github.com/CounterpartyXCP/Documentation/blob/master/Developers/protocol_specification.md