I have my width set to .5mm, and the calibration set to .51 to .52. Since the width/tool path is set to .5, and I'm over extruding just a tad, I get nicely connected lines with parts that hold water. I use .5 just so its a tad easier on the slicer to make smaller walls. Have you tried letting Slic3r adjust the width by itself, by putting 0 for default width? As long as you know you have it dialed in it might clear up some of your issues.
One thing you could try is another slicer. Even though Slic3r is the mainstream now since it's integrated with Repetier Host, I find its not all that accurate sometimes. At the moment I'm trying out Cura, which ships with the Ultimakers. Quite a bit less settings than Slic3r but I'm already seeing improvement in tool paths with it. One key feature is the overlap infill setting which helps connect the infill to perimeters nicely. Not your particular problem but
Bowden SD3, Rumba, E3D hotend, Mk5 with RtRyder changes, Direct drive Y axis and bearings, GT2 pulleys and braided fishing line, Lawsy linear bearing conversion, M3 Z screw.