Lowered the concertible top on my 2003 mercedes clk 430 (just purchased) without a problem. while raising the rear would not lock, so i locked it manually, however the trunk would not open neither manually nor remotely also the switch for the top would not light. managed to open trunk with aux. key. next start up, the trunk worked again, also the switch for the top lights up again but there is no movement of the top in either direction. all fuses are intact. switch is blinking slowly

I have a CLK 2001 and my rear window buttons just work normally when the roof is down. I can even raise a rear window without raising the front one.

https://www.mbusa.com/mercedes/service_and_parts/owners_manuals

foot on the footbrake when doing that.

put you foot on the foot brake as you turn the key.

The remote key has a 2 coin batteries fitted. These may have gone flat. Point the keyfob at the car and watching the key press the unlock button. On the key fob there should be a small LED light which blinks. If not, the batteries need replacing. Try this YouTube video. I think they are CR2025 type batteries.

The top mechanism is hydraulic. Why did you move it manually? Be careful, the hydraulic tubing is plastic and you don't want to apply too much pressure trying to close it, you may damage the tubing. What happens when you try to 'power the top up'? Maybe if you have help pulling it while you try the switch.

On this website you find fuse box diagram and description for Mercedes-Benz CLK

https://www.carknowledge.info/mercedes-benz-clk-class-w209-fuse-box-diagram/

https://www.autogenius.info/mercedes-benz-clk-class-w209-fuse-box/

Tabs at top,lower window prise off

did you recently have a dead battery? Either way try to resynchronize your windows (i'm not sure if you meant front window or rear quarter window). If you hold the window switch in the up position(car running and door closed) untill window reaches the top and continue to hold for 10 seconds the window will reprogram itself. try both front windows. This system is complicated and is best diagnosed via s.d.s. diagnostic machine. I will give you a couple of other possible easy remedies. If your vehicle is equiped with a ski window in the rear trunk panal the door must be shut, also your cargo cover must be shut and plastic lid secured. There are numerous micro switches that input to your soft top control unit-any one could cause the top to be inop. Check to make sure the switch on the cargo cover( retractable cover in trunk) is secured to it's housing, they do periodically fall off. Also if your roll bar ( rear head rests ) has been mechanically deployed You must hold the switch in the up position untill the rams lock back into the roll bar-does the roll bar operate? Always operate top with vehicle running because they are very voltage dependent. Your owners manual will explain how to manually raise top and some simple operation and repair remedies. If you are knowledgable about automotive electrical systems you can disconnect both leads from the battery and touch them together to drain the capacitors and it may reset the module( do not attempt if you are not knowledgable with automotive electricity because there are many things that can go wrong. hopefully I have been helpful.

It is normal for the roll bar to rise when top is down. It seems like the rear valance cover is not secured and the soft op does not understand what position it is in. There is a way to manually close top. it is stated in your owners manual. also I would try to close top with button(assuming your vehicle will start and the battery has good voltage) start car and try to operate top down and try pushing on rear cover also make sure the retractable cover in trunk is extended to compress operation switch