Steele used to recommend the old standby of water resistant or solvent type contact cement and then later they suggested a 3M weatherstrip and trim cement. You might ask them if they still have the same recommendations or now have a better idea. There is an
old thread at AACA where some other recommendations and procedures are discussed. An epoxy adhesive used on floors has one poster saying he had good results. The one shown in the post above by Dell might work well. If you do a search for
runningboard cement several posts in various other old car forums come up asking the same question with more recommendations.
From everything I have read about fresh rubber it continues to emit oils as it dries out so anything you use will require a very thorough cleaning of the rubber before application. As to the grooves, if they are not too deep I would think a waterproof or good quality Bondo might do the job if sanded flush. POR 15 also has a putty like seam sealer and filler that might work better in thick applications but that is probably an expensive overkill. Maybe a coat of POR 15 paint primer would be a good followup over whatever you use to encapsulate and avoid any rust on the metal and also coat and eliminate any porosity in the Bondo or other filler.
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