I believe that your speaker is an old Eminence. I have seen that speaker in some older Mk II's. I was looking at a MK IIB a year or so ago from the original owner who claimed it was all stock with that same speaker. This amp was mint with anvil case, hardwood, EQ Reverb, 60w. Maybe Mesa was using this speaker as an option until the MS-12 was the stock speaker or maybe it was a popular replacement. Call Mesa, Mike B will know. If you like it, leave it alone. Speaker choice can drive you crazy. It is fun though!
The transformer is another story. Dutchman is right. The rust comes from the envirinment it spent it's life in. The rust can be a problem if it gets into the laminate's. It can short out the windings. Ask boogiebabies about a preventative measure. He knows.
Have fun!!