The SN95 ball joints are shorter. If you use Fox ball joints with an SN95 spindle you need a 0.330" spacer between the top of the spindle and the castle nut so it will line up and you can get a cotter pin through the hole.
So yes, if you are going the the SN95 style spindles and changing ball joints then go with the SN95 ball joint. If you want a really good one then go with the low friction design like Maximum Motorsports sells:
If you have deep pockets and want to "improve" the suspension geometry then the Steeda X2's are supposed to be really good:
Steedas X2 greasable ball joints are a longer, stronger ball joint designed to raise the front roll center of your 94-04 S197 and 79-93 fox body Ford Mustang, which becomes lower as a result of lowering the suspension. The X2 ball joint will improve han
www.steeda.com
So $90 for the MM units ($45 ea) or $170 for the Steeda units (sold as a set).