I agree that none of the 3-M products are advisable in this application, but the big issue will (I think) be to get any thixotropic sealant into deep, very narrow grooves such as the OP describes. Not sure how they are located relative to the forces of gravity, but if one really wants to seal the whole groove, using something that will flow "downhill" into the depths of the groove might be better, or something that can be injected via a syringe into the bottom of the groove.
None of these options are easy, but I'd fear that merely trying to force whatever gunk is chosen down from the top would result in a short lifespan for the seal.
Ain't boat ownership
Good luck with whatever you choose, mate.
Jim and Ann s/v Insatiable II lying Sunday Creek, Hinchinbrook Channel, Qld, Oz