Replacing Timing Chain

very likely NOT the timing chain....

 

Welcome to PriusChat!!

How many miles on her?

 

Have you tried accelerating hard to see if the noise is there then as well? If it is, the problem is a blocked catalytic converter, not a timing chain rattle. I replaced the full timing chain, guides, tensioner and water pump (because it had to come out anyway) in my 2008 Gen 2 Prius only to still have the rattle. Turned out to be exhaust pressure build up forcing the engine pipe away from the manifold (held in place with springs compressed as the bolts are tightened) the rapid pressure release causing the springs to slam the pipe back against the manifold, then the pressure build up and the whole pattern repeats. I am a mechanic by trade and it sure sounded like timing chain rattle to me, it is not an easy job to replace the chain and my ex taxi Prius had 720.000km on the clock so it was possible with that sort of mileage on the clock. Once I got it all apart I could see the tensioner hadn't quite reached its full travel and there were no signs of chewed out guides that would have created the metal on metal sound.
If you really want to replace the timing chain, look for a You Tube video for the same engine code to get the idea of what needs to come out, in my case the engine mount was the most trouble, the rest was just a battle to get in between the inner guard/strut tower and the timing cover to get to the hidden bolts. I bought the whole kit on Evil Bay, cheap enough and you can figure out where the bolts are by looking at the replacement gaskets.

T1 Terry

T1 Terry

 

I likely not your chain. Prius gen3 will rattle with clogged egr system.

 

If the engine revs freely on a hill climb, it isn't likely to be the catalytic converter, if it was partially blocked the engine would struggle getting the exhaust gas out and the rattle would be serious.
A dribbling injector could cause a rough run start up and knocking with a slight hydraulic lock or compression that high the fuel in the cyl starts to self ignite. A ruptured fuel pressure regulator diaphragm will do a similar thing but usually doesn't settle down after the motor has run for a few minutes.
A slight head gasket leak allowing water into a cylinder will do a similar thing, is it using water at all or do you see fine bubbles in the radiator?

T1 Terry

 

You may have to take a look at the intake(VVTi) camshaft gear

 

So everything's cleaned on the EGR, all the way back to the Exhaust Manifold connection?

Have you cleaned the intake manifold too? Everything, but in particular the small passageways (about 1/4" diameter at most) at each port. They are the last leg of the EGR circuit.