Often those joints are side-specific, and threaded differently. Don't know specifically on VWs.
Alignment can be WAGged pretty closely by measuring the distances between the tires from back to front. The measurements have to be taken at points the same distance from the ground. (Like at 9 and 3, or 8 and 2: not times,
but spots on a clock face... oh, never mind...)
You want the front of the tires to be SOMETHING LIKE 1/8 of an inch closer than the rear of the tires. Either a VW book or someone in the know can tell you. You can adjust by screwing the rod ends in or out to match. (You didn't tighten the ball joint nuts too tight before adjusting the rod, did you? Hate to see you tear one up trying to adjust it!) Have your steering wheel centered facing straight ahead, and use some kind of straight-edge against the tire to see which side is out of alignment, and adjust that side. You should just have to loosen the clamp nut on the threads just a little to be able to turn the rod end, once the ball joint has been re-disconnected...
I have on occasion counted the number of turns the old one took to come out, and threaded in the new one the same number of turns. That only works well if the new part is made by the same maker...(i.e. same length)