I did mine the exact same way. I left about a 1/2 to 3/4 inch of factory tab sticking up.I then pressure washed the existing factory groove, I was then able to wallow my flap disc Down in there to prep the surfaces for bonding back with thickened resin. Basicly you keep a small portion of the factory tab to create a "track" or template to set your new stringers. I highly suggest you cleats both sides of the stringers. It creates a nice "fat" base to screw and glue your sole too.
http://www.wellcraftv20.com/communit...3&d=1324250018
http://www.wellcraftv20.com/communit...0&d=1325368222
Here are 2 pics. One is showing the factory stringer tab after the stringer was glued in. The second one shows the 3/4 x2 stringer cleats I installed on mine. Go to my build thread and look st pages 7,8,9,10 they show my tabbing and glassing process. You can do this yourself. You just don't want your stringer core making contact with the hull. Good luck and take plenty pictures and keep us updated.