Originally Posted by absRTP
Should I use the ignitor + the BP-Z3 coils ?
No! Absolutely not. You must use one or the other of:
1.8-style coils, wired directly to the Brn and Brn/Yel wires of the vehicle's harness at the point where they would normally enter the igniter, OR
1.6 style coils, with the igniter installed as normal.
To be honest, using the igniter and 1.6 coils is probably going to be beneficial at this stage for the purposes of diagnosis (assuming the under-hood harness has not been hacked up) even if they're just lying on the top of the valve cover. If you're uncertain as to whether they're making contact, you can use a sharp knife to trim away the section of the boot which seals against the valve cover, thus enabling them to be fully inserted. (I've honestly never tried using '90-'00 style plug wires on a VVT valve cover.)
I tried using a timing light on the first spark plug cable with the 1.6 coils and it only does one flash (and a small flash)
This is interesting.
Assuming that your MS is built to the DIY-style plans insofar as the spark driver circuit, then a single spark at power-on is expected. It's an unfortunate side-effect of how they have the circuit designed.
However, if you're not getting any action after that, then it makes me wonder about the software configuration of the MS (presupposing that you have a solid RPM indication while cranking.)
I have seen some timing lights that wouldn't work while the starter was turning, because the starter pulls the battery voltage down too low. So you can try powering the light from an external source (preferably another car battery.)
I still suggest that you at least try swapping the plug wires around, just to be sure that you haven't fallen victim to the 1.6 vs 1.8 mismatch.