weak electrical system

Hi everyone, been away for awhile (which is good I guess) but now I'm back with some problems. Most importantly is my electrical system is weak. The system drags when I try to start it. It holds a weak charge of about 12 volts when running. Rolling down windows seems to put a big enough load on the system to where my headlights dim.
I've put a new battery in, the alternator is 2 years old (checked it at auto store and still good), replaced the starter last year, cleaned all connections, no issues with a short or the ground conn, checked plugs and spark plug wire and all look good. Where do I begin???

12v when running is way low. Should be above 13. Get your own voltmeter and check your alternator again.

Thanks for the reply. Would upgrading to a higher output alternator fix the situation? I don't like it dragging on starts and my headlights dimming when I use my windows

You don't understand the charging system. The 12v has nothing to do with a higher rated alternator. I would go to another auto parts store to get the alternator tested. Read this and educate yourself before you go so you understand the numbers.
http://www.aa1car.com/library/charging_checks.htm

After reading your posts and replies I would suggest replacing both Pos & Neg battery cables. Although the connections maybe clean & tight, there could very well be corrosion under the cable sheathing that is not seen which would cause high resistance in the charging system. A proper charging system will show 14 + volts at the battery terminals with the engine at about 1200 rpm.