Congrats on your fine choice of cars.
Hummm... things to do different or "right the first time"? Ehh?
I would go with the ERA rear differential... the outboard brakes and ease of brake bleeding and pad access is worth it.
I would put the MSD (or ignition box) behind the passenger side of the dashboard.
Like Jim Holden said... INSULATE everything that can be insulated in the footbox area.
I would have a nice Optima battery installed in the trunk in a nice box.
AC pedals.
If staying period correct, then a nice Toploader from Mr Kee.
No windshield washers.
Some sort of shielding put on the rear wheel fender fronts either in invisible or other material.
Make sure that if front
oil cooler is installed that there is a thermal sandwich valve to limit
oil flow to cooler until
oil is hot enough.
After all that I would consider a pre-oiler with dash gauge and selinoid switch to pre oil your engine before startups. (Moroso or Accusump).
Also, you may want to do some serious research and find a CX3 with as many detailed pictures of it and try to "model" you car after it. It is a good learning exercise. Since you live in CA, there are quite a few CX3xxx out there to visit. Bring a camera. Contact the SCCA and get in contact with the Cobra folks in your area.
Cruise Control....
Juss kidden