I don't think filing down a hammer will cause you metallurgical trouble as it isn't a case hardened part. Just remember the firing pin is supposed to finish traveling forward inertially. Before you mess with it at all, check all the usual suspects:
Primers not seated firmly enough are the most common ignition issue. They should all be 0.003" or more below flush with the case head. Seating primers firmly seldom causes a problem, so better to seat too hard than too light. Also, if your cases have been reloaded a bunch of times and you do not routinely clean out the primer pockets, now may be the time. Eventually they can accumulate enough fouling to cushion the primer, thereby interfering with seating and ignition.
Cast bullets sized larger than the chamber throats and seated out far enough to find the throat before the cartridge is fully chambered can interfere with complete chambering. This is because the firing pin blow then pushes the cartridge deeper in the chamber throat by hammering the lead in and the blow is partly absorbed by that.
Both under-seated and and bullet-cushioned rounds usually fire on the second try. That's the symptom to look for. The first attempt finishes seating while the second can then fire against the now firmly positioned primer.
The firing pin tunnel needs to be clean and free of residue or lubricant gum that might impede free and rapid firing pin travel. Spray solvent clean out may help. This is something that works best with extremely thin lube or dry lube or no lube.
Have you tried a more sensitive primer? I find Federals will often fire under circumstances when others don't. This is partly due to cup thickness being on the lean side, partly to actual mix sensitivity, and partly to the cup diameters being a half thousandth or so narrower than some, which allows easier complete seating. Federal recommends that when you feel the primer anvil bottom out in the primer pocket, you seat about 0.002" deeper with this size primer (0.003" deeper for large primers). That's ideal. It slightly compresses the primer pellet between the primer cup and anvil nose, which is called setting the bridge (between the two).
Did you check that the barrel/cylinder gap is adequate size so you know the cylinder isn't too far forward. The gap should be around five or six thousandths. If it is, like, two thousandths or, worse, if you have scrape marks on the cylinder face from dragging on the back of the barrel, then you may need a shim washer that moves the whole cylinder back (a nuisance not to lose when disassembling a single action for cleaning, but sometimes needed if the factory fit was off).
Best bet is to let factory service deal with the mechanical issues. If you have any accuracy complaints, let them check that at the same time. I've had them ream chambers uniform and re-hot blue to factory color, and all free of charge, in response to such a complaint. You're out the Fedex bill, but you get a better gun in that it's had some personal attention from their more knowledgeable employees.