Ok I know there are other threads on this problem but nobody seems to come back with the final solution for their vehicle so I am asking for help with mine.

Mine is a 99 4Runner SR5 3.4 V6 with approx 140000. Got it 6 months ago and service records show the timing belt/water pump service was done at approx 109000. When I got it I did an oil change, seafoam in all 3 places, fuel filter, cleaned the MAF and throttle body, replaced the air filter and got new tires. Was running fine with the exception of a slight squealing when cold but that would go away as it warmed up.

Fast forward to last week. Only drove around 2000 miles since the above things were done. It was fine first thing when it was cold, idle was good no lights. After driving around then stopping for a short period of time then starting it back up and driving, it had a rough idle in park and when stopped. At normal speeds it wasn't rough but power slightly low. On the freeway at speeds over about 80 the check engine light would flash only. Slow down and the CEL stopped. Stop and the idle was rough. Took it home and thought maybe a clogged injector causing a misfire. Seafoam again through the plenum and in the gas tank. Then pulled the EFI fuse and the negative cable on the battery to reset. Drove it around and it ran like a champ. Started right up, no rough idle and no CEL at any speed on freeway. Stopped, turned it off let it set for a couple minutes then started it up. No issues at all. Idle was good. Drove it home on the freeway with no lights no issues so I thought problem solved. Went back out about 2 hrs later to run an errand and the same issues, rough idle, low power and CEL at speeds over 80.

In California you cant get codes read at auto parts stores so I decided to take it to an AAMCO I trusted and get the codes read and a diagnostic. I gave them the same details as above. They called later and said the tech drove around with a scanner on and got codes for a misfire in 2, 3 and 5. Tech recommended replacing two coils and the wires as they are original to the tune of $520. I asked (knowing the answer) if there was a way to troubleshoot without replacing the coils as I thought it was weird they would both go bad at the same time. He said not really they had to start somewhere and that was what the tech recommended. I was disappointed with this answer and said I would pick it up later as I didn't want to throw $520 at the problem hoping that fixes it.

I will get the codes when I pick it up but was hoping for guidance and/or advice from the forum on how I should proceed from here. I feel fairly confident with most do it yourself mechanical stuff on cars and I need to get this running at some point. I'm not made of money though so I can't waste it on hoping to find a solution.

Thanks in advance and I hope I provided enough details.

I will be the first to say it - you need to get the codes and post them here. If it hasn't been done already, you could DIY new plugs, coils, and wires. Unless it has recently been done, I wouldn't replace only the ones in question.

Flashing cel is not good by the way. A steady cel means at least one code was reported. Flashing means stop or else.

Yup, it's worthless to know that there was a CEL without knowing WHAT CEL was thrown. Post up the codes you're throwing, and someone might be able to help.

You can troubleshoot a bad coil by moving it to other cylinders and seeing if the misfire follows the bad coil, but it sounds like you have multiple misfires so that's going to be tough to do.

Good move on telling the shop to not do that work. Although i probably shouldn't be, i'm surprised they didn't at least check the coil packs before offering to replace them.
I had one go bad and cause a misfire at about 120,000 miles. If you have a meter you can easily check them. If you can't find the coil pack specifications, let us know and I'll post them up for you.

Ok so I went to the shop to pick up my 4Runner and here is what I was told.

Initially they checked and there were no codes stored. They are using a snap-on scanner that can give real time data so they drove it around for awhile and were able to get it to read that 2, 3 and 5 cylinders were missing but the car still did not store any codes. All they could get was real time data. They attempted to pull codes from it when I was there with no luck as well. They said it was only when the vehicle was warm and at high speeds that they were able to get the codes and flashing CEL. The CEL would not stay lit either. When I drove it home there was no rough idle, no loss of power and no CEL. I am sure it will happen again when warm. They said the best place to start would be the coils and wires as they were likely the problem. They said it shouldn't be a fuel issue (pump and or injectors) as a fuel flow problem would be there warm or cold.

I am guessing I will tear it apart this week, buy a meter and a code reader and try to troubleshoot it.

Now my questions are:

Does all of this sound right?

What type of meter do I need and what am I looking for on the coils and wires?

Can I just get the cheap scanner that just reads codes?

When I broke a plug wire I had a flashing CEL, I was we'll aware of the problem though.

Change the spark plugs and wires and go from there. It's like $50 for parts.

Thanks John. That sounds like a better idea then trying to troubleshoot and buying a meter and code reader. I found a set of three coil packs new and Bosch wires at an online auto parts warehouse for about $113. Can't hurt to replace all and is a lot cheaper than the $520 they were charging.

Thoughts from everyone?

If 140,000 miles on plugs/wires start there before the coil packs. Use NGK rather than Bosch! Toyota wires have a date printed on them if you want to check if they're truly oe.

I understand NGK is better but at twice the price? Bosch are a name brand and warrantied. Don't see the need to buy NGK...

NGK or Nippondenso plugs, your choice. They're oe to the 4Runner and work, can't say that so reliably for Bosch for either plugs or wires. Make sure you get dual electrode plugs.

An auto parts store will not read codes in CA. They are crazier than when I left!

First off, buy a code reader. They are cheap. Second, if the CEL is on, then there should be a code.

Then yes, follow the advice above., The parts are easy to replace.

If you have an Android smartphone you can get a bluetooth OBD2 dongle for cheap and get the "torque" app for your phone, works really slick, makes me wish you could get it for iphone. Total cost of about $30.

It's best to used the OEM brand replacement parts on any Toyota.

Before you go to swapping parts make sure the injectors are clicking, I had a #2 injector start going bad, and at first it was throwing a #2 misfire code, but as it got worse I did get a #5 and a random misfire code. I think that may have been caused by the off balance oxygen/ fuel sensors trying to compensate for the exhaust sensors readings. Some of the injectors can be checked by touching one end of a long screwdriver to it and holding to your ear. If it's not clicking like the rest, it's not working.

Sorry Habanero...lil miscommunication. Replaced the plugs before and they are OE from Toyota. I was referring to Bosch plug wires which are recommended along with the NGK's.

Vincer77 the CEL does not stay on that must be why no codes. It only flashes when you go over 80. otherwise it's off.

I'm gonna order the coil packs and wires and replace all since I'll be in there and I got a good deal on the coil packs. I'll keep my old ones just in case. That app and OBDII bluetooth sounds like a good idea too. Where do I find it?

In a perfect world you are right about the OEM parts for any vehicle.

Also the injectors doesn't make sense as its an intermittent problem. It would be a misfire all the time if there was an injector problem. That's why it seems more electrical than fuel flow/mix/pattern.