Rough idle and smooth idle

My 99 Civic EX (all stock) with 106K miles and a D16Y8 engine, started rough idling 95% of the time (vibration felt through the steering wheel below 1000 RPM). It runs smooth above 1000 RPM and fuel economy is great. Occasionally the idle drops down to 500 to 600. No codes in the computer. I changed plugs/plug wires, dist. Cap/rotor, air filter, set valve clearances (all were within spec already but reset them anyway), checked and set timing using an SCS connector and service manual (found it 10 degrees too far advanced, reset to 12 degrees before TDC), checked timing belt placement in relation to camshaft pulley and crank pulley, removed/disassembled/cleaned the throttle body, IAC valve, and idle adjust screw (all were dirty), and checked idle speed. I add Chevron Techron to my fuel twice a year. As a last resort I also used Gunk motor flush at last oil change. During cold weather warmup, the engine clacks or chatters. As the outside air temp has been above 65 lately, I notice smoother idling 25% more often than in winter. As a final note, as the fuel tank gets closer to empty, it takes a few more seconds of cranking before the engine will start, and it never did this the first 7 years of ownership.