This type of thing is almost impossible to do from a distance ... so you have to go through stuff you think you know as if you are looking at how someone else did it.
Start by drawing out a wiring diagram - not from memory - by tracing the actual wires.
Something is obviously not as you think it is, so you have to be your own sherlock !
Next ...
why bother with the relay anyway ? you're only powering the coils.
I've wired alternator to reg to 40A fuse to battery to 30A fuse to handlebar switch to ignition packs.
And ...
if the coils are sparking the ignition packs are being fed with a varying signal - which is possibly a rogue connection charging up a capacitor somewhere in the circuit ... so maybe you 'simply' have a poor earth connection causing a current loop you are not aware of ... or maybe you have wired the ignition packs wrongly.
Thats enough thinking for now thanks