Prius rattling, shaking, loud, losing gas mileage, check engine light on

The replaced spark plugs are the correct type and the gap was checked to be proper?

Do you have a friend who has a Gen2 (2004-2009) Prius? If so, I would ask them to allow you to swap a few parts for testing.

P0300 - misfire
P0301 - cyl1 misfire
P0303 - cyl3 misfire
P0304 - cyl4 misfire
You might have 3 bad COPs (Coil Over/On Plug). Cyl2 seems to have a working COP. The ideal test would be to swap a set of working COPs from a known working Prius to yours. If the problem/codes go away, time to order a set of four COPs. Second best test is to swap location of the good COP to each bad COP location with these results:

COP2 and COP1 are exchanged) cyl1 no problem, cyl2 misfires
COP2 and COP3 are exchanged) cyl3 no problem, cyl2 misfires
COP2 and COP4 are exchanged) cyl4 no problem, cyl2 misfires

​

P0171 - system too lean; MAYBE: fuel pump? clogged injector(s)?
How do I fix P0101: Mass or Volume Air Flow Circuit Range/Performance? | PriusChat
Easy test is to swap a freinds Gen2 (2004-2009) Prius MAF into yours. If P0171 goes away, time for a new MAF sensor.

 

Changed plugs.... GOOD. Re-used old COP boots = BAD

I would pull the COPs out and replace the boots with new (Yes, they are readily available and inexpensive), be SURE to use a liberal amount of "di-electric grease" on the inside of the boots (slightly less than a toothpaste amount per boot) and a light coating on the outside.

Sparkplug boots often tear or develop microscopic high voltage leaks when you pull on them for removal, this is MUCH more common when the boots are recessed into the cylinder head, like is done on most modern engines. Add to that, forgetting to use dielectric grease and you are nearly assured of getting misfires.

 

how many miles on her?

 

When I tuned up my 07 I replaced the plugs and replaced all 4 cops with oem cops. Sometimes just taking the cop out the rubber boot is stuck to the plug and you damage the boot. You may not even notice it.Cops are one of the most common replacement parts.
I don't mind spending the extra money on all new cops its been a really good car for the last 11 years so to me it deserves it. Nothing worse then doing all that work and 2 miles down the road you have a misfire and have to tear it all apart again.

It was when i replaced the plugs I found out I have a valve cover gasket leak as it had oil in #3 spark well. And also found both pcv hoses had bad rubber ends the ends were cracked and not sealing right at the valve cover. You really cant see it without taking it all apart to get to the plugs.

New Denso plugs new cops new hoses cleaned the tb and it runs perfect. Have not got to the valve cover gasket yet. Just got the gasket in so maybe this weekend.
I will take pictures of the valve train and post.