Leave the filter in... It will throw off the readings of the MAF... Removing the intake resonator might make an improvement, although it seems to run pretty well... 
1999 Mystique LS V6
Alpine CDA-9807, Rear deck sub, Opt. TB, K&N RU-3530/MAF adaptor, custom heatshield, FSVT 17's, SCT 4-program chip, Eibach's/ST200's, Hella Fogs...
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