Inner stems

Steven-

I usually use a bit of thickened epoxy to tidy up the stem area before glassing the inside of the hull, when I'm sanding the inside. 

The strips are glued to the stems with wood glue (Titebond/Elmers/yellow- PVA) and epoxy will prevent that from bonding, so I wouldn't advise pre-coating the stems with epoxy.

A seal coat before glassing the inside should be enough even if there are voids in the glass.

I used to run into some trouble areas on the shear and once in a while on the inner stem since I always strip to favor the outside joint.

My cloth is laid in the hull with some clothes pins holding it in place. I pull back the cloth and use some thickened epoxy putty on my finger and smooth / fill and areas that have a gap or trouble area. Put the cloth back and begin my wet out. No sanding or worry about bonding / blush. If you have an area where you are worried about the cloth pulling away (not good contact) smear a bit of thickened epoxy putty there first.and that cloth will be held in place. Fortunately these problems only occur on the inside.

I do the same as Jay explains.

Often I use a separate piece of bias cut cloth (4-8" wide ?) in the ends and 'massage' it into thickened epoxy. The 'main' piece of glass just overlaps that end piece - it saves problems with glass shifting, managing overlaps with wet cloth, etc..

The ends are the strongest parts of the boat, so as long as there are no places for water to get into the wood core, and no sharp bits to puncture dry bags (and hands!) I wouldn't worry about the details too much.

BTW, I usually use a gouge and sanding drum to shape the inside of the stems before glassing. It helps to save weight and reduce the amount of epoxy filler needed. If you need something for deck hardware (U-bolt) or through hole  you can add a separate wood block in the appropriate spot, rather than making the stem bigger.