Filling holes and staining the sides

Prior to encapsulating the hull with epoxy I had two cosmetic tasks to complete.  One, I had to fill and sand all the screw holes and two, I needed to stain the sides that would be finished bright. This means it would not be painted since I wanted the mahogany wood to show through.   On the bottom, which would eventually be painted, I used normal wood filler.  However, on the side and transom I wanted the screw holes to match the mahogany and be as "invisible" as possible.  To do that, I used Famowood in mahogany tone, which was recommended in some boat building forums. 
To make sure the filled holes match I did some experimentation.  I filled a hole in a scrap of mahogany plywood and sanded it when dry.  It matched the plywood almost perfectly so I covered it with epoxy but the contrast changed dramatically.   This is shown in the lower left of the picture.  The filled holes, covered with epoxy, are much darker than the plywood. This would make it obvious where each screw was located so I needed a better method.  I then got some water based mahogany stain and repeated the experiment. The match was much closer and is shown in the middle of the picture.  The one filled hole is barely visible so that is the technique I decided to use.

Here is the hull filled and sanded.  It took two passes on the filler to get a smooth finish.  I used a random orbital sander to sand the filler flush.   Attaching a shop vac to the sander to suck up the dust made a big difference.

The next step was to stain the sides and transom. I used a water based wiping mahogany stain from Minwax. Here is a shot of the side showing the difference the stain makes compared to the raw plywood.  As you can see from the first picture, the difference, once epoxied, is much less noticeable.

I'm counting on the epoxy to make the Famowood filler, which is evident in the transom on the last picture, disappear. The stain needed to dry before encapsulating but the weather turned cold and into the 40's so I couldn't proceed even if I wanted.  
There was one other problem, while staining I found a crack in the plywood on the side near the transom.  This needs to be addressed and will be discussed in the next post.