While cranking do you have a value greater than 0 in "Cranking advance (degrees)" in "more ignition options?" If so the timing while cranking will be off by whatever value that is.
One person grounded every 2 out of 3 teeth, added a hall effect sensor and made it a 30-1. http://forums.hybridz.org/topic/77233-30-1-tooth-wheel-with-cherry-hall-effect-sensor/
Another section in here http://forums.hybridz.org/topic/23244-megasquirtnspark-mssmsns-installation-guide/ talks about removing the wheel and re-drilling the alignment hole and rotate the wheel by one whole so you know it's about 72 degrees.
Are you looking at the service manual? It's suppose to go open as soon as the throttle is depressed. You should have a automatic 240sx tps, one with a wire a pigtail coming out of it, since you're on a stock ecu.
Yeah when I have the CHTS unplugged mine would run pig rich. There's not much to the inside of the AFM. The Throttle position switch should open when the throttle is depressed.
Cant really look it up for you right now but take a look at the wiring diagram and follow the wires. http://www.atlanticz.ca/zclub/techtips/wiringdiagrams/74_260z_manual_wire.gif
You'll have to look at the combination switch ( turns on the lights). The fuses and wires for the headlights and running lights.
It's possible the max232 chip burned up... What size resistors were you using as injector resistors? You can test your serial cable by hooking up tx and rx together and see if your computer is transmitting and receiving.