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A new wax ring(I have even had to use 2 at times) should take care of the leak problem,or making a plywood base to raise the base up(a piece of treated plywood cut to the exact size of the base)
you can use a thicker wax ring and this will help but the best thing to do here besides remove the flange is to get a flange extender, its the same size but about a 1/2 thick, it fastens on the existing flange via screws. you can get them at lowes or other home centers