Maybe I missed something. If you had the timing gear marks aligned properly, and did not subsequently remove one of the gears (thereby establishing a new relationship between the crank and cam), this is not a timing gear issue. Rotating the engine to a new position to check for binding would not have changed the relationship of the gears to each other.

Assuming the above to be true, and if all you had to do to make the engine run properly was change the spark plug wires around, you simply have a distributor-to-cam relationship issue. This can be corrected by pulling the distributor, then disengaging the oil pump drive, and re-engaging it in a position 180 degrees from where it was (without rolling the engine over, obviously). This will now cause you to turn the distributor shaft 180 degrees to install it (due to the offset drive slot in the distributor), then you can put the plug wires back where they belong, with the #1 wire pointing towards the front of the engine.
--

Gary L - 1971 142E ITB racer, 73 1800ES, 02 S60 T5
BlueBrick Racing