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Rough running

I have a Toyota 4 Runner 1999,97,777 miles. I have spent $2,000 this month. Tune up, water pump and everything that goes along with that. My car will run fine at first,when I turn it off go into grocery whatever then start it again it runs very rough w/check engine light coming on and off.I got a misfire code on the 4th cyliner that is why I had all spark plugs replaced. But this is still happening my repair shop has no idea what this could be and I am quickly running our of money. Can anyone help, I did fill the car up with gas the night before this happend. Thanks

Well, it really sounds like your repair shop has reached the limits of their expertise, and if you keep going to them, you will also reach the limits of your financial resources.

Take the vehicle to an auto parts retailer (Auto Zone, Advance Auto, NAPA, O’Reilly) that does free scans of your OBD II system. Write down the trouble codes that they give you (the format is akin to P0123), and come back to this thread to report the codes to us. One or more of our experienced mechanics will help to come up with a solution, based on those trouble codes. Then, seek out a new shop with a good reputation to take the vehicle to for the recommended repairs.

I agree with VDC, but I have to ask. Were the spark plug wires replaced?

yes they were, I did take it to Auto Zone and the code was for cylinder 4 the same as before the tune up. Could this be bad gas… I just filled the car with shell v5 premium gas and put a fuel line injector cleaner in it. I’m lost and for what else to do, do you think I should cut my losses and go to a dealership?

If bad gas was the problem, you would have problems in all of the cylinders.
Premium gas will only help if the vehicle actually requires premium, rather than regular gas.
Injector cleaner may help to some extent, but it is unlikely to resolve the problem.

Rather than the dealership, seek out a different independent mechanic. The Car Talk home page has a search engine to find mechanics in your area code.

Thanks for all your help, much appreciated, I went to Car Talk found another garage from your list and will try them. Crossing my fingers.