Thumping noise in engine

My 02 Windstar has developed an intermittent thumping noise in the engine. A bit of history: She has been sitting for a few months because she was throwing a P303 code that I could not track down. Here in IL, you cannot renew your plates until you pass an emissions check, and you cannot pass the check if a code is stored. Well, I got a warning ticket for expired plates, and I had my daughter's car as alternate transportation while she is in the Peace Corps, so I parked Mr. Breeze, intending to get to her on the weekend. Except for throwing the code and gas mileage being a bit down, she was running fine when I parked her.

Well, life happened, and I never seemed to be able to put the time aside, but now winter is coming and I don't want to subject her ride to the snow, so I made time and replaced the coil, plugs, and wires. But when I started her up, there is an intermittent thumping noise in the engine compartment.
I have double checked the wires, and I think I have them right. As I understand it, the right bank plug wires go on the coil towers 1,2,3. and the left bank wires go on the towers 6,5,4. Is that right?

I made a short video so you could hear it, but it is too big to upload, so here's a YouTube. https://www.youtube.com/watch?v=lhewejll_3o&feature=youtu.be

Any thoughts?

Hmmm.... Perhaps an intermittent misfire?

Has it thrown codes since you replaced parts?

I've been afraid to run it long enough for it to throw codes.

I HIGHLY recommend picking up a stethoscope. It's all of $4 at harbor freight and you'll be amazed at how helpful it is in tracking down the source of noises.

http://www.harborfreight.com/mechanics-stethoscope-69913.html

It's hard to tell much from that video but it could be the plastic piece inside the upper intake has broken loose. A stethoscope will rule that in or out quickly.

Just for kicks, remove the auxiliary belt and see if the noise persists.

Thanks for the replies. I will pick up a stethoscope and try her without the belt and report back. Won't be until this week-end, tho, its already dark by the time I get off work.

I agree with the prior suggestions. What is the hose/wire that runs along the intake manifold, then curls under the fuel lines? It appears to shake when the noise occurs.

sounds like it's backfiring through the intake manifold could possibly have a crossed wire but hard to diagnose from a short video

What is the hose/wire that runs along the intake manifold, then curls under the fuel lines? It appears to shake when the noise occurs.

I think what you are looking at is the alternator cable. Actually, the whole engine moves when the Noise occurs.

sounds like it's backfiring through the intake manifold could possibly have a crossed wire but hard to diagnose from a short video

Do I have the right order on the coil? 1-2-3 for the right bank, and 5-6-4 for the left?

Yes, I think you have it right. The engine is laid out from front to back ... the right bank 1-2-3, and the left bank 4-5-6. The front of the engine being where the auxiliary belt is. The left bank is one closer to radiator. The coil pack has three coils ... the end-terminals of each coil can go to either plug in a pair. The "front" (of vehicle) coil supplies plugs in cylinders- 1 & 5; the middle coil- cylinders 2 & 6; the rear coil- cylinders 3 & 4.

Thank you, 12 OZ. I will triple check the routing of the wires.

This image helps me keep it straight. (Not sure where I found it but credit to whomever made it!)

53151

If it is a misfire into the intake, then one possibility is a sticking intake valve. A sticking valve can be confirmed with a intake vacuum test gauge.

You might consider using an engine oil flush to cure it. I don't normally like to use anything added to engine oil, but these flushes are intended to work so that the engine is not damaged (as long as you follow the instructions), and they are known to clear issues with clogged lifters and such.

Another option is to run it for a while to see if the sticking valve will clear itself. The varnish and other deposits could have hardened in the engine if it was sitting for a long time.

Thank you, Tomj. Would Seafoam be suitable for an oil flush? Or is there something else that you would suggest?

I would only use a product that is designed to be added to the engine oil.

There are lots of products available, (for example Gunk Motor Flush which I believe I've used), but I'd do some research to understand what they can be expected to accomplish and how they work before choosing and using one.

You'll have to run the engine for a 10-15 minutes with the flush in the oil, then drain it and replace the oil.

Since you need to run the engine a "long time" to do the flush, you might want to try to run it for some length of time (long enough to reach normal operating temperature?) in hope that the thump will go away without the flush.

Thank you to everyone who posted. It turned out to be crossed plug wires after all. Somehow, I had gotten the cylinder numbering mixed up in my head, and crossed the #4 and #6 wires. Surprising that it idled as smoothly as it did. Now to run her on the road and hopefully she won't set the misfire code any more.