R4 is for the cam sensor, does nothing to help with the crank signal - try R2.
For the earlier (~99) 1.6 cars with the hall effect cam sensor set JPT2 to the 2-3 position. All pinouts are the same in other respects except these cars have no KS among other wires.
Use the FSM to determine the tach wire, refer to the AEM manual to configure one of your LSx outputs as a tach driver.
Frankly, you should use the AEM to turn the alternator on and skip all the diode sillyness... I'll leave that for you guys to figure out, but I assure you it's not difficult.
edit: I'm going to go back on my statement having the AEM control the *generator*. The difference between a generator and an alternator is a built-in regulator. The Protege already has a transistor to control the stator's fielding, but the ECU is supposed to control it. For a generic modern alternator (I just dissected a Honda one) the regulator controls the voltage even without the ECU, although the ECU typically has a provision for being able to fiddle the field windings. I'm not entirely certain right this moment if I should try to run an off-the-shelf regulator on top of the existing generator (and would this require I remove the field control transistor?) or build a circuit to control it. Regardless, both are mundane applications of theory and nothing more.