Then go for it, release just another altcoin and see how it will turn out. You can release some kind of test network first, just to check if your theory works in practice.

You can make it backward-compatible, just by producing first-phase blocks as today and adding some rules to enforce second-phase for these blocks. The simplest way to do that could be using difficulty to decide, how long the second nonce should be. Then you have previous block hash with some zeros, you can place your second-phase nonce there, then taking a single 80-byte block header is enough.

For example:
Because you can see 0x1d value in the difficulty, you know that you can take three bytes from the previous block hash and there must be zeroes to be valid. Also, there is no need for adding any public key to the block header, because it is already calculated in the merkle root. Also, you can add more fields to each header in the coinbase transaction if you really need them, there is no need to add them directly to your headers.