Leave the 3S-GE dizzy in there, just take the cap and rotor off. Then make a low profile cover for it on the lathe.
If you already have a aftermarket computer, it will be easy to run 4 coils, or two twin coils, or 4 coil-on-plug things.
Then you have to remove all the rear water housings also and modify that setup.
One mate mounted the motor a fair way back, and kept the dizzy cap and stock water setup, and just cut his firewall heaps. It is a nightmare to work on, don't do this.
Mount the motor in a normal position, low profile dizzy cover, 4 coils, modifyed water setup.