Power Loss And Vibration Noise Help

Best place to come to with my question! Hopefully my fellow stang fans can help me with this.

I have a manual 05 GT with 291,xxx miles. It has been running flawlessly ever since I got it. Unfortunately the other day I noticed something was wrong. I'm hearing a strange vibration noise coming from what I believe is the engine compartment (not all the time).

The only time I hear this noise is when I --- a) disengage the clutch when shifting from 1-2 or 2-3, .... or b) when I am cruising in 2nd or 3rd and let off the gas. The noise will occur for 1-2 seconds then stop. The more concerning part is that I'm feeling a huge power loss in 2nd gear. It feels bogged down in 2nd, mostly around 2-3k RPMs, although if I keep accelerating, the power does kick in. It is very inconsistent. Sometimes the car runs perfectly fine, but most of the time this is happening. I've been waiting for a CEL to pop up, but still nothing and I've driven over 300 miles while its been going on.

Any help would be greatly appreciated. I'm running a 93 octane race tune from BAMA, with an O/R Pypes H pipe and Borla Stinger catback.
 
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When was the last time the throttle body and MAF sensor cleaned? I would start there if they have not been cleaned for awhile.

How many miles on the spark plugs?
 
Thanks for responses guys. I thought about the engine mounts. Haven't checked them yet but I will do that next. As for the MAF sensor and TB, I just cleaned over the summer, so I don't think that's the issue, but I did think about that. The spark plugs have not been changed since I've got the car at 247,xxx miles. How many miles do spark plugs normally go for?

@Bullitt95 - Would worn engine mounts cause an inconsistent loss in power? Sometimes it still screams without hesitation, but it does seem to be getting worse.
 
To be honest, I changed my plugs out when I installed a supercharger at just over 60k miles and they were worn out, with about .080 to .090 gap, way too much. Would be nice to know how many miles are on those plugs. Might want to pull a few to see what they look like, but be warned about the fact that these plugs are prone to breaking off in the head because of the carbon build up at the tips. Be sure to do plenty of research on the plug changing process and make sure you understand and follow it perfectly. If you are going to pay someone to have the plugs changed be sure they understand the process completely as well.
 
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To be honest, I changed my plugs out when I installed a supercharger at just over 60k miles and they were worn out, with about .080 to .090 gap, way too much. Would be nice to know how many miles are on those plugs. Might want to pull a few to see what they look like, but be warned about the fact that these plugs are prone to breaking off in the head because of the carbon build up at the tips. Be sure to do plenty of research on the plug changing process and make sure you understand and follow it perfectly. If you are going to pay someone to have the plugs changed be sure they understand the process completely as well.

Thank you for the suggestion @cmann ! I will make sure I look into it a lot before changing them. My guess is that there are a lot of miles on these plugs, so that may be the culprit.

I had a similar problem over the summer where a header clamp popped off and gave the same symptoms, but it threw a CEL after a couple hours and gave me a rough idle, so I'm counting that out. I'll check spark plugs and motor mounts this week and post results as soon as I find out.
 
Something else you might consider is the possibility of a bad alternator, which is also know for causing missfire issues.

And if all else fails, (and I'm totally jealous of this as I live way over in western Canada) you are very close to Brenspeed in Pierceton, IN that is possibly one of the best Mustang shops on the continent. Might want to contant them if you can'y figure out what is going on.
 
One more thing to consider. Info from another forum from a member that was seeing his engine bog down in the 2000 to 3000 rpm range, (the difference is that he did get a CEL and code which directed them to a certain cylinder misfire.) states that in looking at things such as the plug, coil etc. his mechanic noticed a lot of "carbon build up" or "carbon tracking" in the spark plug well and on the outside of the coil top itself. he said they cleaned it all up and the problem seemed to have gone away. Now, he is not positive this has permanently solved the issue he was having but its been a couple of days now and he has not reported back so far that the issue has returned. Then again it might have just been removing and reinstalling the coil that may have corrected things.

I'll keep you posted as to what happens going forward.
 
One more thing to consider. Info from another forum from a member that was seeing his engine bog down in the 2000 to 3000 rpm range, (the difference is that he did get a CEL and code which directed them to a certain cylinder misfire.) states that in looking at things such as the plug, coil etc. his mechanic noticed a lot of "carbon build up" or "carbon tracking" in the spark plug well and on the outside of the coil top itself. he said they cleaned it all up and the problem seemed to have gone away. Now, he is not positive this has permanently solved the issue he was having but its been a couple of days now and he has not reported back so far that the issue has returned. Then again it might have just been removing and reinstalling the coil that may have corrected things.

I'll keep you posted as to what happens going forward.

Excellent information. Yeah I think it's strange that I'm not getting a CEL yet. I really want it to throw a code at me to give me some type of guidance! I will keep you updated on what I find out. Not sure when it may be but hopefully very soon.
 
Haven't gotten back to you guys yet, but I DID get my problem fixed! :)
My CEL eventually threw a code for a cylinder misfire and I changed the coil on the cylinder that was showing a code. Amazing how much power was being lost. Unfortunately, I ended up getting a speeding ticket romping on it right outside of town, but I'm just happy by problem was solved!

Thanks everyone for your help :SN: