i'm following you to a point.
in support of using the 36-1 trigger wheel for the basis of engine timing, it is much more precise to run it directly connected to the crankshaft. that gets rid of the negative effects of stretch in the timing belt causing inaccuracies in the timing count.
with the timing set up by a 36-1 wheel on the crank, the cam angle sensor only needs a single pulse occurring in the proximity of the top dead center position of the cam but outside of the corresponding location of the gap for the missing tooth and tooth #1 on the crankshaft. that means that you wouldn't time the cam angle pulse to coincide with missing tooth gap that spans 10 degrees of crank rotation. given that you usually position the missing tooth gap preceding the actual tdc of the crank position (a good rule of thumb being about twice the number of degrees as your projected ignition timing advance) you generally wouldn't run into that clash of electrical timing marks.
the only link i can give you for pics of that as an assembly are in my turbo3 thread. that link is in my sig line at the bottom of my posts.
if you use the stock cas or distributor as the cam angle sensor along with the toothed trigger wheel, you will still need to use the additional circuit to support the hall effect device. that involves using a 4n25 optoisolator to condition the signal. no matter what voltage your hall effect sensor outputs, you use it to fire the led in the opto package. you use a pull up resistor to ensure that the hall effect device fires the led. the led in turn flashes a phototransistor in the opto package that provides the signal that is applied to the pin on the processor at jp10. there is a small ccomponent count circuit that sets up bias and serves as a chopper circuit for that signal.
then you would use tuner studio to set the code to dual wheel, second input at cam speed, etc. that way the main count is established by the crankshaft and the secondary count is set by that single pulse from the cam sensor. refer to the hall effect section in the ms2 manual. scroll down to "second input" for circuit descriptions.
http://www.msextra.com/doc/ms2extra/MS2 ... n.htm#hallit appears that no matter what hall effect device you use, you still have to use a pull up resistor as part of the signal conditioning. that engineering involves knowing what current the hall effect device will handle as a load and as a current sink and choosing resistance values that bias the hall device accordingly. here's an informative link:
http://www.honeywell-sensor.com.cn/prod ... apter4.pdffor my project i had investigated the possibility of using the cas from a late model sohc 16v that mounts on the tail end of the camshaft location. mike cove sent me a link to photos of the ends of the suzuki line of cams and i decided that due to differences in the cam, the cas idea wasn't a good one. i pursued my own vision of something that would be easier and more efficient. my technique is documented in my turbo3 thread and you are more than welcome to adapt it for your use.
i would tend to support your thought of converting to the crank mounted trigger wheel. you'll learn a lot while doing that and you'll also get the hang of the dual trigger wheel implementation. keep in mind that there's really only a couple of good reasons to use the cam angle sensor signal anyway when you use the crank trigger wheel - cop ignition instead of wasted spark and sequential injection. since you're doing a 4 cylinder, wasted spark operation is easier (spark plus in multiples of 2 sets) and the megasquirt already has 2 channels of injection available in it's standard configuration.
other than that, i can't really help you with your engineering too much as i can't be "hands on" with your set up.
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, I was using the wrong pin on the harness 
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