I would say to keep them in the original orientation (spring in) and to remove the RTV from the pitting and put in JB weld to fill the pitting. Then come in and smooth it carefully back to the original level with 180-grit or finer sandpaper to the original level. I have done this before on other aluminum casting and met with more success than with other filler options. The issue I have had previously was that the aluminum would continue to corrode under things like RTV. If you come in and remove the RTV with a small carbide burr in a dremel tool then fill with JB weld it will seal the air and water out of the porosity and give a much longer lasting seal.
I would also recommend to check the shaft diameter with calipers and verify that the seal Inner dimension is at least 1mm smaller than the shaft diameter so that the lips have good positive force against the shaft which will prevent water intrusion.
On my Maramu I filled the area on the outside of the gearbox (where the plastic mounting ring sits) with waterproof grease to help keep water from pooling around the shaft and causing corrosion of the shaft. My shafts were very bad around the seal to the point that I had to buy new gearboxes which will be installed when I return to my boat this fall.
Windward/ Leeward Is.