Is this Podocarpus Japanese yew dead?

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But scratch some of the bark on a limb closer to the trunk and see if it is green underneath.

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Do this and if is still green the branches are still alive - at least for the time being. But keep checking it periodically through the winter. If it is root rot the plant usually won’t recover and the cambium layer under the bark will no longer be green but brown (= dead). If you find after a few months a significant number of the limbs are dead then replace it. Fall and Winter are a good time to plant shrubs anyway so you don’t have to rush it.

I'm certain some is still alive.

I'd wait till Spring and see what sprouts. Then prune as necessary.