most likely the different shift feel is just the diffferent type of linkage. I have driven both quite a bit (parents 95 mystique, my 2000 SE) and it seems like whatever one I drive the most recently I like better so try driving it quite a bit then going back to your SVT and see if the SVT feels funny then.
2000 Silver SE Sport V6 MTX, B&M shifter, SVT exhaust, 75K on the clock.
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