Yes you can use 31 spline axles in it. I have 35 spline in my race car. The shafts will never be to thick for the housing. You just need to make sure if you have a fox body you get fox body length axles. If you have an SN95 get SN95 length axles etc.
Thanks. I have a 96 GT. so as long is I stick to the sn95 it will work. Just so I know I was thinking of a 99 explorer 31 spline I take it that it won't work. And is there a difference in the IDR axle shaft in the 03 cobra.
If you are talking about the differential of the 99exploder I don't see why it wouldn't work. Do some research though. You will still need mustang length axles and NO, cobra half shafts are not even close to working in a solid rear end.