Is the filler really blue or is it the photography? I wish you would have tried one spot before doing the whole wall. It would have been a lot easier to mix color with the filler to match the paneling before applying it. Then all that would be needed is to sand it smooth and clear coat it.
If the filler is white I would mix a universal tinting color with water and color the spots with that. You should be able to color the putty and wipe off the excess off the surrounding wood since it has a finish on it. When you start putting a finish on it you might find it isn't yellow enough. The old varnish on the wall has undoubtly yellowed over the years. If you need to re-create this you can apply some amber shellac to the putty spots with a artist brush. If you plan to use polyurethane over the wall be sure to get some de-waxed amber shellac. The de-waxed version may be more difficult to find but polyurethane won't adhere to standard shellac.
From this point in an inconspicious place I would test one spot with the stain and finish to see if you have the finish procedure worked out before doing the entire wall. It takes a lot of tinkering to mix stain colors. If you can't acquire universal tinting colors you could use acrylic artist paints. You will need yellow oxide with a very little green and a little black.