More Proto4 changes

[akumanatt]

No description provided.

[indigodarkwolf]

I can't recall where, but I know we had a conversation with folks about whether this was the correct approach to clock stretching, and given how the CPU is currently simulated, this seems correct. I'm not sure if this will be a hazard for @ziplantil and pull request #437, but I'm going to go ahead and accept this PR anyways because it represents known hardware changes.

@ziplantil, I apologize if it seems like your PR has been left to stew; that was not my intention, and I'm sure it wasn't Michael's intention, either. I am sure I didn't get a notification from Github when it was flipped over to "ready", and by the time I noticed, there was a bunch of other stuff submitted that I knew was being anticipated by folks in the wider community.