All good advise above. Perhaps try the gun assembled with the stock off and you might see what's happening. I would coat the hammers with a black sharpie and see if they rub inside the frame.
I would also have the original springs put back in the gun since the over powered springs did not solve the problem. The heavy springs may set off a chain of events that will cause additional problems. Primarily excess wear to the bent and sear nose.
I'm not a gunsmith but I've been keeping my old doubles going for a long time. I bet you'll find the answer and it will be something simple. Please let us know since someone else may have the same problem.
+1 on returning to the old springs. No need for new problems.
I have a similar problem on an 1885 Winchester target rifle that is equally vexing. It has a titanium, short-fall hammer that uses both coil and flat springs. After years of flawless service, it is suddenly giving me sporadic light strikes. Cleaning did not help. Protrusion is fine. But something is amiss.