The white power is just corrosion. On a different note, You should have left the bell housing on the trans and unbolted the bell housing from the engine to remove it all as an assembly. Technically, when swapping bell housings, or reinstalling your old one, you need to index it to centerline of the input shaft using a dial indicator.
I understand there are probably alignment dowls and such, but those only get you so close. It depends on how OCD you are if you actually decide to do the process. I know some will tell you not to worry about it. Its a procedure mostly done in high HP cars, but depending on your plans for this CJ it may be something you would want to look into.