Looks like there are a few missing project files for APEX (https://github.com/EpicGames/UnrealEngine/tree/master/Engine/Source/ThirdParty/PhysX/APEX-1.3/compiler/vc12win64-PhysX_3.3)? Specifically the Legacy, Loader and Particles ones.
Am I supposed to get these from somewhere else? If I just try to build as is (with some changes) I get errors with Legacy dll not getting built.
On a different note looks like a few absolute paths were left in APEX_Clothing.vcxproj. Easy to overlook so thought I’d point it out 
<Command Condition="'$(Configuration)|$(Platform)'=='debug|x64'">cl.exe /c /Zi /Ox /MD /arch:AVX /Fd"$(TargetDir)\$(TargetName).pdb" /FoD:/Builds/UE4/Engine/Source/ThirdParty/PhysX/APEX-1.3/compiler/Win64/VS2013/build/x64/APEX_Clothing/debug/avx/SwSolveConstraints.obj ..\..\module\clothing\embedded\LowLevelCloth\src\avx\SwSolveConstraints.cpp</Command>
I just changed them from “D:/Builds/UE4/Engine/Source/ThirdParty/PhysX/APEX-1.3/compiler/Win64/VS2013/build…” to “$(ProjectDir)build…” locally.