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I updated tests to use v0.0.2 release:

https://rawgit.com/andreasplesch/cobweb/cc30beaeb64fae1fb88df65ddc33eb5b338d3d95/cobweb.js/tests/VR/Basic_Inline.xhtml
https://rawgit.com/andreasplesch/cobweb/783c67d2ca2a16302d926d7931469d16ed898feb/cobweb.js/tests/VR/world.html
https://rawgit.com/andreasplesch/cobweb/783c67d2ca2a16302d926d7931469d16ed898feb/cobweb.js/tests/VR/Basic.html
https://rawgit.com/andreasplesch/cobweb/783c67d2ca2a16302d926d7931469d16ed898feb/cobweb.js/tests/VR/PosInterp.html

As you have observed, the camera seems very close and performance is degraded. Are you traversing for each eye separately now ?
Only using the webvr emulator, I see that the canvas is now taking up the whole screen:

<canvas width="3024" height="1680" tabindex="0" style="display: block; width: 3024px; height: 1680px;"></canvas>

which would tend to slow down things.
Manually, in the developer tools, resetting the canvas size to the original:

<canvas width="768" height="432" tabindex="0" style="display: block; width: 768px; height: 432px;"></canvas>

actually gets the frame rate back up, so I guess the large canvas is a factor. Also, the distance looks better.

While HMD pose changes are ok and lead to continuous updates, mouse interactions now provoke a type error:

c08d02e4-2ddc-11e7-83ac-e7fe94008dad.js?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAISTNZ…:53 Uncaught TypeError: Cannot read property '0' of undefined(…)
assign @ …:67
traverse @ …:76
traverse @ …:67
onmotion @ …:67
dispatch @ …:50

The following issues may be related to the hacky approach of separate vrViewMatrix in shaders + using X3DRenderObject to drive all VR:

• Background not properly shaded
• Objects incorrectly not getting added to list of objects to draw
• Lighting shifts with head movement in the Mall
• Cobweb deciding not to draw new frames. Most observable in the Club. Cobweb needs to be informed that moving stuff exists?

Might be better to rework to have WebVR modify existing internal matrices.

Thanks for providing the build.
I quickly put together a minimal scene using your build in a branch of my cobweb fork:
https://github.com/andreasplesch/cobweb/blob/vr-work/cobweb.js/tests/VR/Basic.html
rawgit lets you directly serve:
https://rawgit.com/andreasplesch/cobweb/vr-work/cobweb.js/tests/VR/Basic.html
With spites excellent webvr emulator chrome extension - https://github.com/spite/WebVR-Extension - the scene looks like this:

Nice ! What I noticed is that the frames are only updating on mouseover, at least with the webvr extension. Eg. if one moves the HMD (in the extension) the frame is only updated when mouse is over the canvas. With an actual HMD one could just leave the mouse pointer there. Is that what you do ?