The challenge is to make any significant improvements to the hull finish with the canvas in place. Almost any product that is used to sort out the stain and remaining varnish will seep through and possibly ruin the canvas or the finish and filler. Acids, cleaners (TSP) all need to be flushed with lot's of water. That water will soak through. Non-Phosphate TSP is probably the safest thing that could be used that would minimally damage the canvas. You might try it if a small spot where it won't stand out. I generally experiment under the seats or under the decks.
Until the canvas is off you really cannot attempt anything that would substantially improved the coloration or draw out the stain that was applied. Consequently (assuming you are leaving the canvas on) I would carefully clean the inside of the boat with water and a soft brush. You may decide to use the TSP after testing it on a spot. Then you need to let the boat completely dry out. Next you should sand the wood taking care not to get too aggressive. Since you are not stripping the wood, you should not expect sanding to alter the color. You don't want to sand enough to sand down the cliched tacks. Once it is lightly sanded, varnish it.
A Captains Spar tends to be a lighter/brighter varnish than the darker/richer Epifanes. You might consider that as the one to use. Do not use polyurethane. Use only marine grade spar varnish on your boat.
Whatever you apply, the stain and wood will darken up. Hopefully it won't look black.
I would apply three (or more) coats. The first couple should be thinned following the manufacturers instruction. A few years from now when you replace the canvas you can properly strip the hull, TeakNu, TSP etc. Personally I never use linseed oil inside the hull...thinned varnish on the inside, occasionally shellac for coloring, warmed/hot boiled linseed, mineral spirits and turpentine blend on the outside.
You should post some pictures.
