Couple of ideas!
Greg:If you are going to tighten the toe rail bolts, I would suggest that you do it with a torque wrench. You may want to contact Hunter and see if they have any spec's. You want it tighened but do not overtighten, this may compress all of the sealant out of the joint. As Frank mentioned you may need to recaulk the joint but hopefully not.As far as the companion way goes. The track is an open channel, open on both ends. If you have the time to correct the problem correctly, you would need to remove the sea hood and then seal the forward end of the channel. This is a very big job and you take the chance of damage to the sea hood. As an alternative we just clean ours out to make sure that water can drain from the aft end of the track. Also make sure that the drains are clear of mud, dirt leaves etc. Then we had a cover made for the companion way. This keeps the water from getting on the companionway to begin with. The obvious problems will still occur if you wash the boat down without the cover in place. This also helps keep the interior of the boat much cleaner.