Huge gaps on walls of my print - Prusa Mendel i3

I've built and maintained my printer for about two years now. I have upgraded the hotend to a E3D and have had great results before. I recently have been getting these large gaps where the it wouldn't seem to extrude at all and just skip entirely. I have tried tweaking retraction, shells, z starting points and used different slic3r programs (Slic3r and Cura) with no real change. This has appeared in models similar to this and the best I can do is patch it with putty. Is there a problem with the model itself? The stl file is that this set [www.thingiverse.com] , filename is TechWallCornerA for picture 1 and TechWallA for picture 2 and 3. Any help is appreciated!

Have you tried changing the infill to a higher %?

I had a similar problem with a Marvin Keyring where the section under his face area would be flattened and if I turn off the PLC cooling fan when it does this area, it would print perfect, but with the cooling fan on in this area it would cause it to collapse inside and 10%-50% infill had no change. Are you using a cooling fan when you print this area?

Just some thoughts...