Wood Epoxy

After the excess glue is removed, it's time to see where epoxy repair is needed.  The epoxy is a 2 part putty epoxy that sticks and dries to wood very well.  The holes and dents need to be prepared by removing any dust or debris with tack cloth.  Tack cloth is recommended only for areas where a reside is ok.  This stuff leaves a sticky resin on the wood that makes the epoxy stick.  I wouldn't use it to prep for painting, because the residue would create problems for the finish.

Here is a video of me using Tack Cloth.

This is the kind of epoxy I used.

Wear rubber gloves when you use this stuff.  Only mix equal parts to make a blob about 1 in. in diameter.
If you mix too much at once, it will start to harden before you use it all unless you're filling large holes.
This stuff is rock hard and can be chiseled and sanded just like wood.  The best part is is won't come out of holes and shallow dents.  It acts just like it's part of the wood around it, except it's harder.  You have to be careful not to damage the wood around it when trying to shape it due to the differences in hardness between the epoxy and wood.  Once you paint it, it disappears.  I can't see any of the nail holes I filled in the vertical trim pieces.

Here is a video of me applying the wood epoxy.

One note - I only use epoxy filler on sashes and areas that will be exposed to water or sun.  The cracked areas of the sill are a good example of where to use epoxy.  The interior parts that need patching, like the horizontal pieces above the window where the old curtain fixtures were removed, were patched with a regular wood putty because it's way easier to sand down.

After shaping and sanding everything down good with 100 then 150 grit sandpaper, it's time to prime the wood in the areas that will be painted.