David,
Do you have any interior leaks that seem to originate from the underside of the cap-rail / hull deck joint? Or drip from fasteners along the hull deck joint? Or that run down along the interior of the hull?
Pilgrim had leaks of this nature in the pilot berth area, behind the electrical panel, and in the quarterberth area. The leaks were caused by water running between the teak caprail and the fiberglass hull/deck joint. The water entered at poorly installed bow cleats, bow pulpit stanchions, and a failed seam behind the rub rails. Since you have removed to rub rails and stripped the wood not is the time to address any apparent issues.
- Inspect all hardware mounted on cap rail to ensure it is properly bedded. Removing it now for repairs will only make your re-finishing job easier.
- seal any gaps or openings in the joint between the upper and lower pieces on the cap rail.
On Pilgrim the majority of water finding it's way under the cap rail was doing so via the butt joint between the two pieces of wood. I can see from your images that some areas of this joint are opening up. Pilgrim's looked much worse than Namaste's. Ours were so bad we resorted to removing a section of teak and gluing splines onto the joint. Check out our blog posts on the project...
Minor joint failure, as it appears you have in some of the images, could be remedied by using a syringe to inject thickened epoxy into the opened seam. Fill any extra or loose screw holes in the cap rail while you've got the syringe loaded up.
Are you certain the rub rails are aluminum and not stainless steel? Aluminum is a rather soft metal and would be a poor choice for a rub rail.
From you description above it sounds like you plan to re-install the rub rails then apply varnish or Cetol over the rail... correct? Perhaps I misunderstood your intentions. Best to avoid applying a wood coating to a metal object. Why not complete all the coats on the wood, then re-install the rail. This will make it much easier to apply the coating while keeping the coating off of the metal.
Keep silicone products away from the bare wood! If any silicone comes in contact with the wood then it will be very difficult to fully remove. The residual silicone will prohibit the varnish / cetol from bonding with the wood. There are very few good applications for silicone on a marine vessel. Best to use butyl tape, 3M's 4000UV, or a similar Sikaflex product when sealing or bedding above the waterline.
Don't forget to metal polish the rail prior to re-installing. Much easier to polish while off the vessel. I highly recommend
Collinite Metal Wax. If you really want to go all the way then use a buffing wheel on an bench grinder to polish both the rub rail and the screw heads.
Per application and number of coats - follow the instructions on the product to the letter. You are conducting a chemistry project. The manufacture has spent a great deal of time figuring out how best to apply their product.
Good luck and keep posting updates so we can follow along with your progress.
Jeff