I also have a new 5 speed (2000, not mustang)and replaced the stock with a adjustable short shifter.
The legal jargon in the warranty on my car basically states that the dealer must prove that the modification or alteration was the source of the problem that led to the failure of the warranteed item.
If they tell you that your short shifter was the cause of your rear end blowing out, well, I'd call a lawyer.
my 2 cents
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