I went through about 25 links to different threads with different bits of information in each of them while looking for a direct how-to on this, myself.
From those sources, members of this forum, my own experience, and a completely random source I lucked into, I thought I would create a simple, straight-forward guide on this process, since these tops are prone to numerous issues that will at some point require manually opening/closing your top. I tried this multiple times to confirm. Using the quickest method, estimated total time is 5-10 minutes.
So here is my guide: How to raise the rear windows and lock the trunk/boot latches after manually opening/closing the top. (We can start with the rear quarter windows, as these are likely the biggest concern in regards to rain/immediate necessity of the vehicle. Then we will move on to the trunk.)
1. To raise the rear windows, do not have your roof latched yet. If it is manually latched/locked, unlock it.
2. You are going to imitate the last step of the top operation manually, WHILE holding down the button. This does require two people, unless you're just really skilled,
. So, just to repeat : Hold the red top button forward, as if you're closing the top. While holding that, have another individual push the roof into position and lock it with the hex key.
3. Keep holding down the button, the car will assume it has reached this stage in the operation, and the rear windows will raise. If it doesn't work the first time, try it again.
*Notes: for the well-being of your pump, as you will run the pump, ensure the pump screw is tightened (don't leave it loose), and that there is at least some fluid in it. Yes, it will leak out if your cylinders are at fault, but at least it eliminates much of the risk of damaging the pump by running it dry. However, if you have no fluid, you can actually run the pump briefly without causing damage; but I wouldn't recommend it, especially not for longer than a few seconds. If you need to fill the pump a little, there are plenty of great guides here, and you don't have to remove the side panels or anything to do it, either; just need a syringe and 1/4" OD tubing.
Trunk latches :
There are two ways to get this done, one requires removing the trunk interior panels, the other method does not. That's right, it's possible without removing the panels. There's less room to work this way, but in an emergency and in a hurry, it works.
1. In this step, determine which you'd prefer. You can either remove the trunk panels, this will give you the most room to work with, or you can simply remove the little trunk panel doors on the left and right side (the small panels that give you access to the pull cables/pump/etc.) Either way, you want to do all of this while the trunk is in the standard open position, so if you remove the panels, be sure to put the trunk back down, and open it as you would normally (grocery-mode as some say.)
2. Loosen the pump screw all the way. Essentially, all you have to do is compress the gold part of the hydraulic cylinders up all the way. (The bottoms of the cylinders have a little bracket, that, when down, pushes against the cable that keeps the locks from locking.) However, this can be very tough to compress these by hand sometimes, and even tougher if you don't take the side panels off. I will detail how to do both below:
3a. (SIDE PANELS REMOVED) : Pull the little pin out of each cylinder. Just use your thumb, and it pops off, and slides out. Very, very easy. Lift the trunk arm/bracket on each side just a tiny bit and slide the hydraulic cylinder to the left/right (whichever gives your more space with it.)
4a. (SIDE PANELS REMOVED) : Now, you can run a screwdriver through the holes of the top of the cylinder, use this as a T-handle to compress/decompress the cylinder to where when the base is pulled all the way up, it lines up with the hole on the arm/bracket/tubular frame. Do NOT put it back on yet. Tuck it away somewhere it won't be in the way.
5a. (SIDE PANELS REMOVED) : Put all of the panels back on, except the little door panels (that give access to the cables/pump/etc.)
6a. (SIDE PANELS REMOVED) : Reach one hand in, with your other hand carefully lifting the frame on each side just an inch, slide the hydraulic cylinder in line with the frame. (just opposite of how you moved it out to the side, before.) Simply put the pin through the cylinder top and frame, and now it is ready to lock. (the cylinder will be all the way up, and no longer putting downward pressure on the cable.)
3b. (SIDE PANELS NOT REMOVED) : Reach through the panel door openings, you will be able to see and reach each cylinder. At the top of the cylinder, you will feel little tabs for the pin, simply push these back, and the pin can be slid right out from the cylinder. Try not to drop these pins, and take them out.
4b. (SIDE PANELS NOT REMOVED) : Lift the trunk arm/bracket on each side just a tiny bit and slide the hydraulic cylinder to the left/right (whichever gives your more space with it.)
5b. (SIDE PANELS NOT REMOVED) : Now is completely up to you, you can take the easiest route, and zip tie the cylinder in the up position (you'll feel that you can slide the entire cylinder down, and back up - you want it all the way up). There are several things to tie it to, even the same frame-hole the pin was in (you can use two hands, as you can also reach this through the "brush" section. OR, you can take the much more difficult route, and try to compress the cylinders by hand, adjust them to line up with the holes while in the 'up' position, and then reinsert the pins in that position.
6. Now, all that's left is locking it. You'll notice, even with these cylinders in the up position, you may not get a "lock" when you put the seat belt latches into the holes. This is where analyzing this video (attached) is important. These latches actually get pulled in, and backwards (towards the rear of the car.) So apply downward pressure to each frame/arm and latch, and also pull backwards. It will lock, and you are done.
Assuming you use the zip tie method, you can have your windows up and trunk locked in about 5-10 minutes, with no problems.
Assuming there are no other problems at hand (electronically, or with worn down latches, etc.), this will solve both of these problems. I'm hoping I was pretty thorough and didn't leave too much out. Attached are several pictures and a video that correlate to this guide.
Hopefully, this helps you not have to dig all over the internet when trying to solve this problem. This is a problem every slk owner may have to deal with, and I hope this is helpful to some!
Many of the pics are from google/pelican parts. If you haven't checked out their site, I highly recommend it for R170 picture guides, and several other cars!
Mercedes-Benz SLK-Class R170 (1998-2004) Technical Articles ? Pelican Parts