YDoesGodMockMeSo,
Looks good so far. I used the JPM from the download section (other than the handle, I don't see much diffence between the JPM and the JEM, except for maybe the JEM has a deeper cutaway maybe) to make the body below. As far as suggestions, just do what you want with the routes, it is your guitar.
lovekraft,
When you have used the CA to fill, have you ever had any problems with staining or tung oiling? Does the glue create "gaps" or "streaks" from not taking the stain or oil?