When you got the bike running with the main fuse blown, it was running on the stator/regulator without the battery.
The battery does a bunch of things on the bike, and one of them is stabilizing the voltage. So it is probable that while you were running without the battery, the bikes voltage was swinging widely up and down ... way over 12 volts at times.
My guess is that this could have blown the ignition module (assuming your bike is like mine and has a transistorised ignition).
That would explain why both coils (and a new coil) would not spark.
My OEM manual for a 650 has a fairly simple test for ignition modules. If you are curious enough to want to check your old ignition just to see, I'll dig it up and post it.
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