I ran my times last year manually shifting, but that's only because I found out that the 6200 and 6400 rpm shift points are WAY too low. It was simply a crutch for having a chitty tune and I still couldn't shift to 7k. Technically, these cars should NOT be manually shifted.
With your Vortech setup, your shift points need to be up there. 7K rpms is the max. Even with my setup, I think that 6500 rpms is still short shifting. If you are at 6000-6200 rpms, you need to go higher. WAY higher.
I think that you'll also find that with a Cobra intake, you are going to be making more power in the upper range than you are with your stock manifold now and will benefit even more from the higher shift points. The forced induction is somewhat blanketing the manifold issue to a certain extent, but it's still there. Just a thought.
Between that and a better stall converter choice with higher shift points in the tune, low 12s would be very attainable I would think. And don't forget the driver mod.