PhatTony,
220amp alternator at what RPM? Some HO alternators don't put out their rated power untill they reach roughly 3000 RPM. Any less than that, and they are no better than stock. Are you using the same pully? Larger diameter pully = Less RPM @ alt. = Less output...Just a thought.
You replaced the wire from alt. to battery positive, engine block to frame and frame to battery negative...what guage wire?
In my experiance, a second battery does not do much if you dont listen to the stereo with the motor turned off. Some might argue that it does strengthen the electrical system a bit, but thats debatable. In your case (unless you plan on listening to the system with the motor off) it would be a band aid for a larger problem.
If the alt. is rated to put out 220 @ idle AND you used proper guage wire all around (Big 3, power, ground etc.) AND all your connections are sound, then I would say that either your alt is going out or your alt isn't big enough.
The only thing that a yellow top will do is allow you to drain the battery and recharge without damage to the cells. I don't think that this is the answer to your voltage problem.
How big was your stock alt?
Did you grind off ALL paint, dirt, rust etc. then clean the metal with paint thinner for ALL of your ground/electrical connections?
Have any connecton come loose?
How old is your battery?
What kind of vehicle?
These are my thoughts on your situation.