Hello! Welcome to the site! Thanks for coming! I'm Ron Z. I'm here to provide as much information and insight as I can, to best answer your question.
From what you are describing here, this can be a few things. First, having the Diagnostic Trouble Codes (the codes stored in the computer that are setting the Check Engine
light) would help a ton in the diagnostic flow here. These codes help to better pinpoint that actual system that has the fault and will better pinpoint the best way to correct the problem. If you do not have these trouble codes, then I can try to give as much insight with the information you've provided.
First, this very well could be a problem with spark plugs. Toyota recommends they are replaced at every 96,000km. So if they haven't been replaced in a while, this very well could be a possible cause. On this vehice a very common problem is a faulty Ignition Coil
as well. These coils sit on top of the spark plugs and when faulty will creat a cylinder misfire (this is where those trouble codes would come in handy!) and produce loss ofengine performance. So these should be tested as well.
As for the Fuel Injection system needing a flush- this isn't very common, but if the vehicle had sat for a long time, or only made short trips, or wasn't used that often, this "could" play a role in it. Whether or not it is actually a reason for the problem... could go either way.
As for the Converter- if you had the original replaced, and they used a "universal" or a "low quality" Converter, this could also be a contributor of the problem. A universal or low quality converter doesn't meet Toyota specs and will usually fail or get "clogged" in a short amount of time which can definitely lead to engine performance issues. The reason why the Dealer needs to replace the Front Pipe, is this is the "correct" version that "should" be installed. The Converter is built into a part of the front pipe assembly.
As for the price- I'm seeing the plugs sell for around $3.50 each (you need 6) and the labor time guide calls for just about 2 hours to complete the job. The Injection Flush is usually a set price as a service, and will vary from shop to shop, but the average is around $125-$175 for the service. The Converter (the correct version as part of the front pipe) sells for around $400 or so. The labr time guide calls for just about an hour to complete the job. Labor rates vary from shop to shop, so what you pay for labor will effect the botXXXXX XXXXXne. For a job of this type, a "fair" labor rate can by anywhere from $85-$125 per hour. SO, the estimate you were given does seem a little high.
Again, having those trouble codes would help us eliminate un-needed things like the Injector system flush or the need for a new Converter.
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