Love those Dean Markley pickups. I'm surprised that you didn't run into more phase issues mixing the mic with the pickup that way- these guitars sound crystal clear. On a related note- the fact that "And Became Invisible" has 200 tracks and still sounds as focused and coherent as it does speaks volumes of your production chops. Gaddamn.
Never worked with Reaper- how's the learning curve? More importantly, is it affordable?