Another thought I had is if the safety is able to be even partially engaged with the hammer down it might prevent the hammer hooks from clearing the sear and would prevent the hammer from cocking. You should never engage the safety with the hammer down or at half cock. With factory parts you shouldn't be able to engage the safety with the hammer down. If the sear has been replaced with an adjustable sear from CGW it is possible to engage the safety with the hammer down but is not advised as it can do damage to the sear hammer interface.
Is this a stock gun? Have you done any polishing to parts in the action? If no, can you apply the safety with the hammer down? If yes, then you may need a new sear, safety lever, hammer or all of it.
No trouble at all. We're here to help you. The more info you are able to share the better and easier it will be to help troubleshoot.
Cheers,
Toby