2002 Prius Misfiring, Hybrid sytem warning lights have come on

So my car has been through two sets of spark plugs and it still seems to misfire after long and frequent stops. I I deliver meds to nursing homes so I do alot of miles. The hybrid system lights have come on once in a while, about 3 times in the last 3 months. I took it to the dealer and they said that the check engine light was on due to the misfire. They told me that they received a code for the hybrid system computer which is still covered under the warranty. They told me that the misfire could be causing the hybrid system computer code to come up. They told me to replace the spark plugs so I did. Well, now the car is still misfiring, although not as much, and they told me that it could be a coil pack, I have already replaced one coil pack on my own. Also, they told me that it the check engine light comes on again then I should bring it back in because it might really be the computer that needs to be replaced. What should I make of all of this? Should they really be replacing the computer now and they are just giving me the business? Please help!