Chrysler Repair: severe engine noise: 3.5L

Question
QUESTION: My 2010 Chrysler 300 with 3.5 engine developed a severe engine noise.  I thought it was a rod or broken rocker arm.  Had the car towed home and replaced rocker arm assembly on the drivers side. Put back on what I needed to start the car and it sounded great.  Put the intake plenum back on and the noise started again.  It sounded terrible, but more on the passenger side.  Very metallic sounding. Like valves bouncing off pistons. I checked the rocker assembly on the passenger side and it was getting plenty of oil. If I take the intake off it sounds fine.  Took the actuator off the short running valve and it sounds good. If I turn the SRV by hand no difference.  If I put my hand over the front where the actuator attaches creating a suction, then the noise starts again. Any suggestions?s

ANSWER: All I can suggest is to examine the timing belt sprocket markings with the engine at TDC to see if there may be an issue with a misalignment alignment of the camshafts with the crankshaft. I don't understand what you are observing as far as the change in the noise is concerned but somehow it may be that something has slipped one tooth.

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QUESTION: Checked the timing (what a pain), but the alignment of both camshaft marks were perfect.  I am getting a code of 0113, no letter "P" in front. Would a bad Intake Air Temperature Sensor cause the problems I described?

ANSWER: Hi Gary,
No, I don't see how that sensor would do that noise issue.
By the way, sorry to ask but when you checked the cam marks to be aligned with one another were you sure that the crank was at TDC? I believe that one manual shows that rather than determining where the crank is from a mark on the crank sprocket that instead you use a dial indicator inserted in cyl 1 spark plug hole to determine TDC. If you are certain the crank was at top TDC then I wouldn't go through it again as you indicate it is a pain to do.
Roland

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QUESTION: Roland,
    Confident the crank was at TDC.  Timing belt was good and tight with no cracking and no water pump leakage.  The problem seems to be no air getting into the intake making the engine clatter really bad.

Answer
Hi Gary,
I have to beg ignorance of what might be able to cause the noise.
The short runner valve according to the manual energizes a mechanical linkage that allows the intake air to be redirect to six "short runners". It only is supposed to occur about 5,000 rpm and wide open throttle. I have not been 'inside' the intake manifold to see how this works, but could the mechanical linkage some how be coming in contact with the valves?
I wonder if an engine rebuilding shop familiar with the 3.5L engine might not be a resource. If you can drive it to such a shop someone might be able to identify the cause. Do let me know when you find out.
Thanks.
Roland