The position of the #1 spark plug wire in the distributor cap is not necessarily a function of the alignment of the timing gear dots. When the dots are aligned at the timing chain (top sprocket dot at the bottom and the crankshaft dot at the top) the rotor should be pointing at the #6 terminal inside the cap. If you rotate the crankshaft 360 degrees (so that both dots are at the top of their respective orbits) the rotor should be pointing to #1. While the crankshaft/camshaft are thusly aligned, you will be able to loosen the distributor, lift it clear of the cam gear and turn the rotor to any position you'd prefer. Just make sure that you re-position the wires so that the rotor is aligned with the number # 1 spark plug wire in the cap (at whatever position you've chosen around the clock). Then, follow up by inserting the rest of the plug wires clockwise around the cap in the sequence of the firing order. The last step would be to adjust the timing with a timing light as usual.
On second thought, if it's running well and you're not terminally upset with the precise positioning of the wires, I'd just leave it alone. I have realized that I could make this change in my sleep but explaining it isn't so easy. I have a lot of admiration for the people who write tech manuals.
