Best way to clean out water jackets

The "best" way, which is what you asked, is to take the block to the machine shop.

I doubt they are going to take the time (or the customer is willing to pay for the time) to physically pick away at the scale in a block much than right at the freeze plug holes.

You can acid and chemical wash and even pressure wash to your hearts content. But large scale needs to be physically picked out the block.

If you are going to half fill it, I'd really make sure the remaining water passages were spotless.

long screwdriver, coat hanger, radiator hose pick, etc...and your hard work, patience, and attention to detail.