If your SVT has the 'premium sound' option and you are sure they didn't use any kind of bypass harness then I would take your car back to them and raise a little hell(not much, just a little). Not bypassing that amp could seriously damage it. The noise you hear may be related to the un-bypassed amp...not sure though so don't qoute me. Hope this helps.
Peace,
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Brad W.
98.5 SE
KKM True-Rev--Narva Bulbs
99 SVT Wheels--BFG g-Force T/A KDW
Custom Acoustics
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"There are some things so serious you have to laugh at them."