I have a '97 4-runner. I had wires and plugs installed. Since then the engine has had a ticking sound. We had the flywheel replaced, water pump and timing belt replaced. $2000 later it is still ticking. It runs like a dream but the “ticking” is annoying.
You did not state the vehicle mileage, which engine you have, or if the ticking is present at all times or only on acceleration but since the vehicle appears to run fine my feeling is that the wires/plugs replacement is not related to the ticking.
My feeling is that what you’re hearing is a valve lash tick. Valve lash should be inspected and adjusted as necessary every 30k miles at most. There are a number of reasons why valve lash can become excessive and it only takes one valve with too much clearance to become a major irritant.
Have you had a mechanic specifically look for the ticking problem? Given that it started right after you had the plugs and wires replaced, it could be as simple as a loose spark plug wire. What can happen is that the little metal part inside the boot where the wire attaches to the spark plug can come loose and leave a gap. This causes the high-voltage electricity to jump across the gap, before traveling down into the spark plug which can cause an audible “tick” every time that cylinder fires. You might try checking (with the engine off) that all the plug wires are on snug both at the plugs and at the distributor or coil.
Anyone check the PCV valve???