First of all, clean your working area. You will lose parts on the floor and if it is as messy as mine you'll end up with less than a complete lock.
The first order of business is to remove the existing seals so that we can get access to the pinstacks. The ABUS65/40 has a single small seal made out of brass on each of the pin chambers. In order to extract these I drilled a small hole in each one using a hand drill. Care should be taken to not drill all the way through the seal or you might damage the delicate springs underneath. Drill one hole in each seal. Then take a screw and fasten it down in the hole with a screwdriver. Once the screw is securely fastened into the soft brass you can extract the seal.

In the image above you can also see the sixth chamber which contains the retainer pin. The retainer pin is a long rod which prevents the plug from being extracted from the shell. You don't have to remove it but it makes it easier to clean the lock from metal filings.
Take care when removing the seal as the springs easily launches out of the lock and gets lost. A pair of pliers makes it easier as you don't have to use as much force. Once the seals are removed you can extract the pins one by one.

The box prevents you from losing any of the small parts and keeps the ground brass from spreading everywhere. You can seal up the holes with masking tape so you don't get the pins mixed up.

Above we can see the extracted pinstacks. I drilled the first holes with a multitool, and this caused me to drill through the first few seals and damage the springs underneath. One spring is also missing; don't repeat these mistakes. Also note the non-spool driver in the first chamber. This prevents the plug from jiggling around in the shell when the key is not inserted.
Now that your lock has been ridden of the pins (and possibly the plug) we can start with the "fancy" part of this mod. We will be cutting M3 threads in the upper parts of the chambers so that we can seal them with screws, much like Medeco does on their cylinders.

I used a simple, cheap thread cutting kit bought from a hardware store (about $12 or so). M3 is a metric thread and it just so happens that it was a perfect fit for this ABUS lock. Your mileage might vary for other locks, but you can always drill up the top of the chambers ever so slightly.
When cutting the threads you need to be careful. Despite brass being soft compared to the steel these tools normally cut it is easy to use too much torque and snap the tool. You must go back and forth with the cutting tool, letting the cut material fall off the tip as to not clog it up. I didn't thread the retainer pin chamber, but is possible to do so and replace the retainer pin with a screw.
Once you have cut threads into all the chambers we can get to the boring part; creating new seals. I simply used some spare M3 threaded rod that I cut into small pieces. I then used my multitool fitted with an abrasive disc to cut a small depression in one end of the rod. This allows a standard flathead screwdriver to interface the rod.

If you can find small screws without a head this would be a neater option (and a real time saver since this cutting and grinding took longer than anything else). I didn't have any though.
And so finally we end up with this:

Notice the retainer pin has been stuffed back in it's chamber as well. The screw seals are uneven because I cut the chambers to different depths and the length of the screws also vary somewhat. This way you can actually create "balanced" pinstacks.
I hope you enjoyed this guide, any suggestions welcome.