MY Z3 roof soft top is not operating either

Looks like a failed relay:
"I sat in the car and started pushing the roll bar button. We heard a click every time I pushed it. My brother was at the back of the car and was trying to hear where the clicking was coming from. He realized it was coming from a relay switch so he took a screwdriver and tapped the top of the relay and **BAM** everything starts working! So through that we realized it was a bad relay".
Fixed my convertible top problems
4RA 007 791 011 4RA007791011 002 542 72 19 0025427219 New Hella Relay...

Thanks to Benzworld.org
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Find the two plastic caps sitting behind the sun visor on either side of the car. Gently prise them out, be careful as years of sun may have made them brittle. Behind the caps you should see a hexagonal head that the manual roof tool fits into (failing that use an allen key). Turning these hex heads will unlock the front soft top locks. (can't recall if it was clockwise or anti-clockwise, so be careful!). I found that you need to start one side, then unlock the other side, then come back to the first side and finish the job off. At this stage you should be able to lift the top up slightly to see it's no longer engaged in the front locks. Now move to the boot.

In the back of the boot you should see two small pieces of the trim that will lift out. These will be located on each side near the boot hinge mechanisms. Lift the trim peices out and you should see a lever (mine is made from cad plated something or other, ie it's a gold colour) and it will have red paint on it.

Fit the spanner/wrench end of the manual roof tool, or otherwise a 10mm open ended spanner, onto the small nut welded into the end of that red lever. I started on the left side(passenger side), levering gently down will unlock, and gently up will lock). You may need to alternate between each side, undoing a little and then swapping. NOTE: I found the levers won't budge unless the soft or hard top 'pins' are physically sitting in the lock holes. Don't force the levers as they should move quite easily.

Now that you have both the front and back locks undone, the last part is to unlock the tonneau or rear deck (soft top roof compartment). To do this you need the 10mm spanner/wrench again. You will find two hex heads tucked down in between the roll bar and the side of the interior trim (about 6-8 inches from the door frames), fit the spanner onto the head and turn until the tonneau cover releases. You should now be able to fold the soft top down by first raising the rear section of the soft top until the back lip is pointing to the sky, then lift the front section along with the rear section down into the compartment. I guess getting it back out is a reverse of the procedure above. Hoepfully I've got it all right as I've done it from memory.

wd40 does miracles

The control module has set a fault and it will have to be reset. They are sensitive to voltage & must have 12 volts to operate properly.
The windows and top will need to be resync. I cannot find any information regarding the diagnostic procedure for the roof .. it states there is a procedure to diagnose the fault with the number of flashes the switch makes .. a dealer may be your best option on this fault .. I hope this helps some.

there is a microswitch on the right side under roof cover if roof cover not fully down boot is locked shut by microswitch you might be able to press on cover and you may here boot lock solinoid click off get some one to push boot lock if you can.t reach when you get in boot /trunk you should see small wire that travels across rear bulkhead disconnect this and trunk/boot lid will open but roof will not obviasly i,ve worked on one of these all day today and have had every thing wrong with roof you could imagine good luck

not real sure on bmw but did you try lowering rear windows first

is your soft top not working it's not the faulty relay, it's control by electronic control unit, it's call soft top control unit, so first do one thing, open boot and have a look, there are one separation lid which is winding like cover, you must have close your boot separation lid buy pulling it out and hang it on hook which is locate both side back in boot, there are two hooks for hookup the separation roller lid,you pull it out and hookup it on two hooks, and close boot then operate roof if still roof not working it's need to be diagnose because there are many sensors and switches are fitted in this system if one switch or sensor not work your roof will not longer be opening and also there are any hydraulic oil leaking or lack of oil in the pump, it will not work, so in this case you must drive your car to the authorized Mercedes workshop who have the right diagnose tool knowledge for this particular car,

Best to take it to a shop or a delaer to get codes, but I think the top latch above the rear view mirror is not clamping down the top tight enough. The second message "Check Soft Top Motion" leads me to believe this - the OBD thinks the top hasn't finished opening/closing. Unfortunately there isn't too much in the way of adjustment that can be done, besides R&R of the microswitches (that you mention are in good shape).

Has the pump got enough oil

i had the same problem and BMW told me it will cost 1200 AUD to fix. I fixed it for free. inside there is a tiny kill switch above the passanger side. it wont let the roof operate unless you lift the roof. that was the problem. it was faulty. I by passed it and it has been fine for 5 years. I can't find the switch to replace so when I watch and lift the roof like you normaly do when want to open it.