Yea you would have to write all the existing code from scratch to start using p-roc or fast or such. Once you spent about a year getting the game rewritten to play as it does now then you could get started.

Johnny would be a cool game for someone to do a software re-write on, though. As the game sits it seems to kind of be dominated by Spinner Millions and Yakuza Strike. Plus I'm not really a fan of the whole cybermatrix awards thing, I think it would be much cooler being a risk/reward type thing to add balls/jackpot value to your multiball, like you stated in your original post.

Anyways, I can't really imagine this ever happening, but hey, we can dream

Pretty sure that's just about what they did with the Ma-y-trix retheme, there are a few around. I don't think they increased the number of balls in the machine though.

Edit:

https://pinside.com/pinball/forum/topic/the-matrix-pinball-machine-pinnovating

As others have said, it's doable with a P-roc or similar