Well done mate.
The Nissan calipers will help rectify the front -> back brake balance. Are your calipers the 4 piston jag ones, I know they are the worst for brake balance in a cobra as they have very large pistons. 48mm pistons from memory. The Nissan calipers have smaller 37mm pistons. Assuming you pedal ratio is similiar to mine, I've calculated with standard jag rotor, that Nissan calipers will give close to perfect brake balance. If you have a larger rotor(like I have bought), then you will need something in between the jag and nissan piston sizes. You can get Wilwoods that are perfect, just slightly larger pistons than the Skyline calipers or 2 piston PBR calipers that have 42mm piston sizes from memory, getting a little on the large size, but still much better than jag 4 piston.
The jag 3 piston calipers have a much better piston size and will help brake balance.
Is your pedal travel feel about right?
I would fix the brake balance first, then see how it all feels.
You can sit down and calculate this stuff, lots of info on the Internet on it. Very time consuming though.