Roof Rack Leak... Fixes?

Well my racks causing the leak in the Heep. I am trying to figure out the best way to seal it up, get new nutserts and seals from Jeep if available, remove the factory rack since I have a surco and gutters and just put the bolts back in with silicone, or fill them in with the old welder and be done with it.... any other ideas I could consider?

take off the rack rails and lay a gob of marine GOOP in and around each insert. put the rails back on and good to go.