Hope you are using anerobic sealant, which won't harden until there is an abscence of oxygen (created when the case halves are torqued together). Should wipe right off with brake cleaner or similar if the halves have not been mated.
It has been years since I split and resealed a SHO trans (felt like brain surgery compared to rebuilding an engine), but vaguely recall something about the shift input rod needing to be in the correct position (and maybe moved as the case halves come together?). I have Bizzy's instructions on how to disassemble, but they do not include much on reassembly other than a warning not to use RTV, and to use Permatex Anerobic instead.