I think this is a classic case of middle aged spread
The 12 was designed in a 2009 world, we are all older now in 2017 and guess what, all the goodies have expanded which results in more wires etc.
We have modified he whole routing and bundling of W-45 and W-46 as it goes down and rearwards because there isn't sufficient room to route it where the original plans say without creating pinch points and stress. We have brought our two bundles down between the rudder horns and tied them forward to an extra cushion clamp on the firewall rather than try and force them over the rudder tubes and down - that would have been nearly impossible at the point in the build when it is prescribed. You may have done it if the two bundles were routed a page or three earlier.
Where they go under the mixer is tight on both of ours and was cured by being diligent in wire routing, literally pulling and laying them one at a time to avoid crossovers and extra lumps.
A little extra bend and fold here and there on the covers helped, as did a small amount of pressure once installed with a piece of 2 x 1 battening to 'scrunch' everything together.
Hope that helps.