Like mentioned, you need to sand both sides of the mating surface to make sure they are as flat as possible, remove high spots created by corrosion, etc.
For the RTV to work properly (and the anti-freeze resistant grey RTV silicone you bought is the best one for the job).
*Both sides have to be cleaned of dirt, corrosion and contaminants. (i.e. sand and clean it).
*Both sides have to be dry and free of contaminants (I use brake cleaner when I can).
*You have 5 minutes after applying the bead to one surface to mate it to the other, to get it to adhere and cure to the other surface as well as the one you applied the bead.
*Once the parts are together, tighten the bolts only finger tight (this will get rtv down to a thin gasket layer, but NOT force all of it out at some high spots.
*Leave it for an hour to cure (that will let the thin layer cure and NOT get forced out when you torque down the parts).
*After an hour to cure, torque the bolts properly.
Obviously temperature effects cure times, the instructions assume this is done at room temp, allow more time for colder, less for hot.
The thickness of the RTV Silicone will effect cure time, the thin layer between the parts, that is essential will cure much faster than the bead of excess that was squeezed out around the edges. So don't get wrapped around the axle about the bead of excess around the edge NOT being fully cured after 24 hours. Usually after an hour it should be cured enough to be put into use, but considering the difficulties you've been having, I would wait a full 24 hours after doing a proper job before using it.