traction control won't hold you back. its just another nice safety feature. however, if you like ripping tyres, making alot of smoke and getting the back to swing out (and you should, its a jz, that's what they're for
then just hit the trac control switch and turn it off. that's what i do. Get a nice LSD to go with it too if you don't already have one
being an auto, you should get a good tranny cooler. one of the best mods you can buy to protect your investment, especially if you plan to up the boost later and you drive aggressively. heat is the biggest killer of autos. i found out the hard way.
sequential to full parallel? its possible, google it. alot of people have done it and its not very hard to do. there is the downside of loosing your low end torque though, the car will feel sluggish until about 4500rpm when you compare it to the sequential setup. if you have the vvt-i version it might not be soo bad in the lower rpm range
build a custom manifold for the twins? hmmm. i guess the real question is why? what power/gains are you hoping to or can achieve by doing that? and then compare that to the cost of going big single or just turning up the boost. that should be what drives your decision. I know there are a few aftermarket manifolds for the vvt-i wun jay (1j) that are designed to use the stock turbo and oem intake/outlet and they provide some great gains but they are expensive.
so let us know how the numbers work out for u and the 2j. it would be nice to know what gains you'd get