Wasn't this in a YJ? Maybe the shifter arm on the case is a different length than a TJ one. Either that, or you're probably going to have to loosen that little adjuster nut on the horribly designed TJ linkage and adjust it for the new case. If that doesn't work, just order a Novak Cable shifter for it.
http://www.novak-adapt.com/catalog/shifters/sk2xc.htm
Why do I still know **** about jeeps?!