Most of my temperature problems stem from the ash buildup when using briquets on a long slow cook. It will start out great hold temperature for a while then slowly creap down. I have the stack extended. Don't have the baffle, but did turn the larger grate in the chamber upside dow to act as a baffle once but couldn't get up to temp. My main problem should be solved by raising the charcoal/fire up off the bottom to allow the ash to fall down and not choke out the fire.
try a basket that holds the fire up off the bottom more than it already is. Your problem seems to be air flow control.
Also, when I started out I didn't have the side fire box and made the fire on one side of the grill, opposite from the stack. worked really well, might be something to try in the meantime.
Char-griller pro deluxe w/SFB
22.5" weber kettle (rescue)