engine’s #2 and#4 are misfiring, what needs to be done/replaced?
Can’t tell over the internet what’s wrong with your engine. It’s a simple engine, most any decent mechanic should be able to figure it out.
Your car has 4 engines? 
The cylinders are misfiring, not the “engines”. Cylinders are just one component of an engine. The misfiring could be caused by poor timing (more likely to affect all cylinders), no/poor spark, a bad wire or wires, or bad ignition coils. I’d have a mechanic take a look at it.
Are there any specific conditions that cause the problem? Does it happen on the highway, in the morning, after fueling up… etc.?
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At 120K miles or so spark plugs had to be replaced… with a proper iridium ones… check if that applies to you
plugs I removed from the same year Prius when I bought it at 117K miles were OK-ish, but definitely needed replacement around their scheduled life
second item to check on this vintage of Prius is a throttle body: it tends to get dirty and leads to rough operation, which can lead to misfires
when getting around throttle body it makes great sense to clean the MAF sensor
also, think if your problem coincides with air filter replacement (by the way, when was it replaced last time??)
the mechanics here is: filter is located right atop MAF and people often incidentally get some debris on it and it throws engine off, once again resulting in rough operations and possibly misfire
Will it idle? When do you get the misfire? How do you know it’s #2 and #4cyl, do you have any other codes. Is it just when eng is cold?