Those tunes look tighter to the valve cover then some others I have seen.
I myself didn't like the 90* bend. I have run them under the tube. Other tubes have a little more room. Depends on the header and the actual bend. (Damm 1 size fits all header!)
The suggestion of a sock is good and what I have done in the past with vari angle boots.

Also to note, the stock wire loom I did not use. It's location is OK. But if you can reposition the wires to stay held within the loom, it would help with positioning the wire itself next to the header tube.