The plan now looks like this:
First step was to extend the helix track out into a position on the Staging Deck area so that I had the right angle/reference point to work from rather than guessing it.
I also changed the turnouts to Peco SL-95 RH Turnouts, the alignment has worked much better, and I have eliminated the S Curves, along with increasing the staging track lengths a little more again.
The entire yard ladder flows much better, and has no S Curves. The staggered alignment of the switches now allows the fronts of any locomotives to be seen while staged too.