Timing trouble on 650sx

Hi guys I currently have a kawasaki 650sx with a total loss system and msd ignition setup. My previous msd ignition box blew up so I've just received my second hand one which I brought off a guy on here. I have spark but the ski will not start it just coughs and splutters I was wondering would the timing be different on the 2 different boxes? And if so how do i check? Any help would be great thanks.
 
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