Mmmmm... no, not right so far.
- If you lined up the dots on the timing chain with the dot on the cam sprocket at 6 o'clock, and the dot on the crank sprocket at 12 o'clock, then both #1 and #6 are at TDC, and it is #6 that is firing with the timing chain sprockets aligned in that manner, not #1.
- You don't rotate the crank to line up the rotor. You keep the crank where it was when you set up the timing chain, and pull up and drop back in intermediate shaft over an over until the slot in the shaft points to the #1 intake bolt as said. THEN you drop in the distributor with the rotor pointing in the opposite direction, which is #6 spark tower.
Do you know if you rotated the crank less than 1 full turn? If so, then rotate it another full turn and then some more until the external (ignition) timing marks line up at 0... so that you are back where you started. (In other words, 2 full turns from where you started.)
Please confirm that you set the timing dots as described above, at 6 and 12 o'clock, so we can be sure what you have. If not, then a valve cover can be removed to get things all sorted out again.
