Trane AC/furnace noise

I have a 2-year old Trane XL80, two-stage gas furnace, Model TUP120R960K, installed horizontally in my basement crawlspace. I also have a relatively new Trane XR13, Model 2TTR3024A, air conditioner with an H- coil mounted about two feet beyond the plenum. (A 5-ton furnace and a 2- ton AC - I live in Canada!)
When the fan is running, for heating or cooling, the furnace generates an annoying rattling sound. I've traced the source to two baffles mounted on the heat exchanger. They vibrate, particularly when the 2nd-stage kicks in.
I had a warranty serviceman in today, and he concurred that it was the baffles that were making the noise and suggested that they could be removed without causing a problem.
I asked him to hold off, because each of the baffles is clearly stamped "DO NOT REMOVE."
According to the serviceman, the baffles are needed for vertical installations, but are not necessarily needed for horizontal installs.
Does that make sense or is he trying to fix the problem at minimal cost to his firm and possibly creating another major one for me down the road?
I also wonder if the problem could be attributable to the design of my plenum. Rather than being a large gently curved elbow, my plenum is a horizontal sheet-metal box measuring 20"W x 30"L x 24"H, on top of which is mounted an elbow measuring 18W x 16"L x 18"H. This is then reduced to ductwork measuring 18"W and 8"H.
I wondering if instead of flowing smoothly through gently curved ducts, air turbulence is being created in the box-shaped plenum, which in turn causes the baffles to vibrate and rattle.
Sorry for being so long winded and thanks for any help you can provide.
Regards,
Morvin
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responding to http://www.homeownershub.com/maintenance/Trane-AC-furnace-noise-128308-.htm kappy32 wrote:
Morvin Stayner wrote:

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Did You ever get a reply as to what to do? I seem to have the same problem.
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Here is the reply:
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