The project files create a megaglest.exe, but for whatever reason, the expected output is glest_game.exe (presumably the original binary as created for vanilla Glest). The various debugging files are also named glest_game.*.
The project file should be updated to use the correct names. With the wrong name, MSVS is not able to run the binary. I'm not entirely sure how the debug files are used, but I imagine that having the wrong name affects them, too.
This is as of rev 31def0dc1ae.