Okay... So I haven't really worked on those before, but they should be very simple.

This might sound stupid but I am assuming its getting fuel because its running although make sure those two cylinders on the right are getting fuel Cylinder 1 and cylinder 2.

Make sure that the coil wires are indeed placed on the correct cylinder.
Here is somewhat of a reference.

Also make sure that the ignition coil didn't move while working on the motor they tend to do that.

Here is a video of someone fixing a similar problem it might or might not help you.
As I said I haven't really worked on them but if they get fuel and fire they should run nothing complex about them.
youtube VW beetle rough running

Last but not least test the coil leads and see if they actually throw a spark out, hold it close to a metal object and see if a spark occurs. It might be hard with those leads, I see they are enclosed. What we usually do is press our pinky in there to see if it will shock us. and then adds the spark plugs and see if they generate a spark.

If both generate a spark, try mixing up the spark plugs and see if that helps, I have had spark plugs that throws a spark out but when you insert it into the chamber the compression inside might break down the spark and then it doesn't ignite the fuel.

I will do some digging around and see if I can come up with something else but that's mainly what there is. Seeing that uncle already tested the compression