After many years struggling in this God forsaken business ( job shop ) I have to say that quoting can be different for every customer you have. Experience will give you a ball park price as long as you know your outside cost, plating, heat treat, grind etc.
Programs, whether CAD/CAM based or spreadsheet based can all be helpful. That said, the bottom line is "what's it take to get the job?". Due to the huge number of variables beyond your control, there is no simple answer.
I do know that it took me 20 years to realize I was in business to make "MONEY", not parts. As much as we all love a challenge and I presume we all love to make parts, that is only a means to an end.