Interestingly enough, my buddy & I have just been going through the exact same issues with our Q4R ignitions on our Ford Zetec engines.
We had sent our bottom pulleys to Ehrlich (years ago, now - we're just getting the engines fired now), who installed reluctor wheels on them. Our first startup attempt (on an engine stand) didn't go well. Set fire to the carbs, and my buddy's shirt. Lots of backfiring.
We messed around with a timing light, and got extremely limited information, because of the "wasted-spark" issue. Plus, like your engine, the Zetec has no timing marks at all.
The wasted-spark thing is weird. The "second" spark is one where the polarity is reversed, and is a fair bit weaker than the "primary" spark. That could cause issues in deciphering the problem.
By the way - the plug wires for #2 and #3 can be swapped at any time, with no affect on running. Same with #1 and #4. This is because each coil fires both plugs wired to it simultaneously.
Our primary issue, though, turns out to be that Ehrlich installed our reluctor wheels 90* out of rotation from where they should have been, so ignition was occurring at 10* after BDC instead of 10* before TDC. Once we rotated the reluctor 90*, the engine fired instantly. Still a bit of fine tuning to do, but we're getting there.
We're also installing timing marks on the reluctor wheels, and timing pointers on the engine itself.
If I can help some, feel free to PM me.
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Scratch building, at continental-drift speed, a custom McSoreley-design framed, dual-Weber 45DCOE carburated, Zetec-engined, ridiculously fast money pit.
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