How do I get my engine to run smooth?

On my 2003 Lincoln LS (V6) I have had to replace sections of the vacuum/hose assembly that runs from the PCV valve, around the back firewall, and up the passenger side to the front of the engine. The parts are not in inventory, so I had to build makeshift hoses/lines. Needless to say, my car runs pretty rough and when diagnosed (parts store) it mentioned the Mass Air Sensor as the problem. I honestly believe that its not breathing correctly, but the extent of my fledgling mechanical ability is coming up fast. Any ideas on what I can do or how much it will cost to get help? Thanks. Rick