That type of gasketed screw typically needs no additional sealant. although it won't hurt to put a little under each head. Unfortunately, replacing the screws may not solve the problem. I have some experience with skylights and overhead, pergola-like structures. Unfortunately, water is very resourceful and, in installations like this, leaks can occur in one place and appear inches or feet away from where you think the problem is. Since you don't explain or show how your structure is constructed, I can't comment more specifically. I just wanted to caution you to not be surprised if you still have leaks after replacing all the screws. It may be necessary to do more or something else to permanently fix it.

Laura, It sounds like you are dealing with contraction joints, not expansion joints. These joints are just meant to control cracking. The self-leveling sealer should work fine, however, I have to be honest I have limited experience with concrete patios. I design large concrete pavements for runways and airports. The applications are a little different. We seal our contraction joints with self-leveling silicone. My only fear is that your expectations might be a little overreaching. Your concrete is always going expand and contract, it's the nature of the beast. The sealer is really meant to eliminate water infiltration, not to provide a completely smooth surface. The troweled joints that you have may be very shallow as well, which might lend to the potential for the sealant to be pulled out due to the lack of vertical surfaces to adhere to. You might want to check with someone who pours concrete patio's or driveways and get their feedback. I don't think it could hurt to try it on a small area though to see if it meets your expectations. Let me know if I can be of any more assistance. Riles

These comments are all very helpful. Thank you. While you were writing these comments, we were meeting with a contractor who is going to address some omissions with the board and batten siding and flashing. He too, concluded that fixing it with pieces of mahogany would be best. I like the idea of the caulk for deep voids as well. We have some leftover trim from the door install (pieces that are are different than the casing). I will go and see this base trim and see if we can fashion some from what we have leftover. Todd -- LOL. I think you are correct that we will never see the mason again as he has been paid in full.

No, the orange foam is filler. Ideally it would be best if you could find some rubber material (circular) to make a cone over that opening. Use the exterior grade caulk to seal it. What ever material you use to do this should be 1 piece, so you will need to find material big enough for this use. Avoid making flat areas where water can pool, the object is to make the water run off. Normally these kinds of openings for line set entry in to a building are typically square chases. Made of sheet metal most common. To seal them there is a sheet metal roof over the top and they normally get sealed with tar like roofing sealer. But if you ever need to open this access point up you'll be glad you didn't use tar like roof sealer.