Death Rattle... clean manifold & EGR, new plugs, no change

Rattling is caused by misfiring. Misfiring is caused by lots of things.

There are some posters who will give more or less confident narrower opinions on the cause based on exactly when your rattling comes and goes. That's one available clue. There are some tests that can identify whether the oft-suspected head gasket is the cause.

Other than that, it's a matter of misfire diagnosis, which is a big topic, with other posts giving more ideas already. Here's one.

 

Those look like pictures of a transmission damper whose coil springs have all been pounded to smithereens (lying in the bellhousing in the lower picture).

Once that has happened, the car will make clatters and rattles just because the damper's got no springs.

Something else was the original cause of the clatter that pounded the springs.

 

I would be pretty surprised ... that aspect of how the Prius 'damper' is built is shared with pretty much every manual transmission clutch disc ever, kind of a mature product space.

I see the mileage was 121k at the start of this thread. One really just doesn't hear of clutch discs turning their springs into rubble over 121k miles for no reason. Could it happen? Well ... never say never.

By the same token, the Prius powertrain does have the feature that any misfiring for any reason, possibly even just in some earlier period of the car's life, works those springs like crazy.

 

And yet the number of Prii that pass 121,000 miles without having pounded their springs into confetti seems rather large.

The "bump" comes from MG1, which can be spun with any amount of torque the ECU chooses to apply.

 

Give it time, make sure the cold start shakes are gone. The damper plate failure "may" have been a consequence of head gasket allowing uncompressible coolant into a combustion chamber. You've remedied the damper, but keep an eye on it. Leak-down test?

 

It was near-certainly a consequence of something causing uneven engine rotation over some period of time; a head gasket issue would be one of the many candidate somethings.