Try adjusting your clutch application.
Have the MGW shifter and still have the clunk, however that is not what I bought it for. I bought it to get a better shifter it is fantastic now very positive engagement and have not missed a single shift since the switch.
like Ltngdrvr posted if you slip the clutch slightly when shifting to 2nd it typically will not clunk.
13 GT base, 3.55, Sterling Grey, MGW shifter, BMR LCA's, GT500 AB, silver RTR's, 275/40/19 Michelin pilot super sports, more stereo equipment than I will admit to, more parts to come.