I think you are better off working with Peter Todd, a bitcoin developer working on opentimestamps (github.com/opentimestamps), rather than inventing your own th

I think you are better off working with Peter Todd, a bitcoin developer working on opentimestamps (github.com/opentimestamps), rather than inventing your own thing. He's already got Merkle tree hashing, and injects data into the Bitcoin blockchain using the standard merged-mining protocol, meaning it doesn't increase the chain size at all (beyond the hit that's already being taken to allowed merged mining of things like Namecoin.)