The way that I would do it is about the same as Norm C's, just a little different as I don't see this as much a problem with the gaps as with the lost tongue material. For the missing wood, take a piece of paper and a soft pencil and, using the edge of the pencil, mark around the hole. Transfer the shape of the missing wood to a similar piece of wood if you can "steal" some. If you don't have enough suitable wood, at least fins some of the same variety. When you have several patterns marked on the new wood, saw it to a thickness about 1/8" thicker than needed on a band saw and then run it through a planer so the finished thickness is about 1/32" thicker than needed. Now glue it in place with Gorilla Glue or the similar TiteBond product. Since this glue expands like crazy as it cures, you will have to weight it down to keep it in place. I use one of my tool boxes for this since they are pretty heavy and put a piece of Saran Wrap om the bottom of the box so the glue doesn't stick to it either. After 24 hours, sand the plugs flush with a belt sander, hand held is OK since these should be small areas or use the big, floor sander, just do it lightly so you don't gouge the floor.
This will take a lot of time but you have a lot of that invested already, Boyd.