Andrew,
First and foremost, congratulations! ERA makes a great Cobra … be it a 427, FIA or Slab Side. For my FIA went the the QuickTime bell housing & TKO 600 with 0.82 OD. Peter recommend the 3.54 rear axle ratio for my 302. You should be fine with a 3.31 rear and 393w, but check with ERA to be sure.
I used the recommended shifter location from ERA, the gearbox can be configured with different shifter locations. The shifter is offset a bit to the right of the transmission tunnel center line, I suspect that a Top Loader shifter would be biased a bit to the left of the center line, due to the external shifter linkage.
Either way, the shifter falls to hand very nicely and it’s a pleasure to row through the gears. I would also recommend the external slave cylinder setup, but a lot of guys like the internal slave cylinder setup (Throwout bearing / slave cylinder combo) as is used in the Corvette for example. They both get the job done.
Here are some photos …