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If you have a gap along the window glass it's because they fit over a plastic ledge. To fit them you have to work from the top and then push the door cards into place from above and down and then starting pushing the base clips in.
Thinking about it are the wipers sat in the parked position before you disconnected the motor? If they weren't positioned correctly the mechanism arms could be sat wrong under the scuttle and fouling something as you try to remove.
Yes 3 bolts along the top and back of the motor there is a grommet and push fit fastener. You need to give this a pull forward to release then angle the whole unit and pull out.
Here is a photo of the grommet thing that is near the motor:
Tha caps can be changed mate. Remove the mirror. Unscrew mirror adjusting platform (3/4 screws I think) and you will see the little plastic tabs that you need to press and push through. The whole mirror unit also needs folding in as there a clip at the far edge.