Tried to capture everything in the subject to help with searches. As suggested I think I’ve cracked the heal and toe issue on the pre-2006 pedal box.
The big problem (for me) was the height difference between the accelerator and the brake pedal when the brake was fully depressed. So, three things to address.
First off fully bleed the brakes and replace fluid. This ensured the pedal was not dropping further than it had to.
Then raised the brake pedal slightly…
Then lowered the accelerator (by about and inch, or 25 mm)
In addition my brake has been moved over slightly to the right to close the gap between the pedals. I may invest in a non-slip pad the the accelerator and maybe a slightly modified accelerator pedal itself.
On the whole this has solved the problem for me and I even happier with the driving experience.
Hard down-shifts are now a joy!