The remote as well as the inside release will not open my trunk. When I use the manual key, turning it to the right and pushing in, it opens the trunk, but also cause all the windows to go down! Additionally, the remote now also doesn't operate the door locks. The trunk / windows routine baffles me the most - any ideas?

 

Make sure that after using the mechanical key to open the trunk that the lock is placed back in the position it was before you opened it. You may also want to check the batteries in the keyfob.

 

Try resetting the pneumatic pump.

Find the interior light just behind the right rear passenger's heels.
Pry the light out, and find the yellow fuse behind it.
Remove the fuse, check it and replace it.

If the door and trunk locks now function, but quit soon afterwards, you probably have a leak in the pneumatic system, usually a failed actuator. Resetting the system allows it to work long enough for troubleshooting.

 

As far as I know, you open the trunk by turning anti-clockwise, and then pushing in, then return to mid-position.
If you turn the key clockwise, you put it in the "valet" mode, meaning you can't open it with the button controls.