It would depend what year dyna. The 06 and up have a wider frame. Also they have pretty different mount points on the trans. The pipes might fit up but the fxr and dyna mids are two separate animals
I have an '08 TC96 2-into-1 on my 1990 Glide, a SuperTrapp. The cylinder head ends bolt right up and the trans cover mounting works just fine. I'm not sure about any rearward mounting, but on my bag frames the muffler also fits OK. Are you talking about a secondhand system, or getting a new one?