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having also followed this for quite a while, i'm sorry to hear about the issues you are having. Hope it comes together ASAP and it running to its true potential.
being in australia and building my own rb26/30 there are numerous cars out there with this style of combination and i can quiet honestly say that none of them use a crank trigger for the ignition signal. these are cars that are making approximately 1000hp and putting down 160mph down the qtr mile. the main difference being they are using the best aftermarket computer available in the world, MOTEC. Seems like a cheap insurance when building such an engine.
The slightly larger honing for cylinders 5 & 6 appears to be a cheap, but costly (excuse the pun) fix for a problem that can be tuned out of the car if the computer/tuner have the options available, being individual injectors control and egt's probes in the exhaust manifold.
this is just something to think about, that's all.
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