OK, here goes:
Sounds like the trolley is not connecting to the cushion arm correctly.
Did you follow this note on page 16:
QUOTE
if the manual release is used, close the door before reactivating the opener.
Also, perhaps the moveable limit stops are not correctly located, maybe by the chain moving after you disconnected the door. I think the motor/chain should operate 'normally' whether or not the door is attached. In other words, the limit stops should cause the motor to run in the proper direction and stop even without the door being connected. Without the door connected, you may have moved the chain inadvertently.
As a final thought, the door arm assembly seems to be adjustable in length. Perhaps a 'helper' shortened it for you by screwing the two pieces together more than needed.
Other than the above, I note that you may have been using British tools on this device. I'm not sure, but since the device was made in the USA(!), you may need to use only American screwdrivers, hammers, and wrenches. I think those types all work from the left side as opposed to the right! Also, in America, we use 'right is tight' to remember which way to turn a screw/bolt/nut. Is that also different 'over there?!'