When I had my drive shaft shortened for my "new" transmission, the shop that I took it to noticed that the u-joints were not "in phase" as mentioned in the link above. They brought it to the attention of the senior member of the shop who said that he remembered that back in the day Firebirds were built with that and there was some good reason for it. He wasn't sure just what the reason was but he said it had to be that way. They were very careful to re-assemble the shaft exactly as it was. Could this slight defference be there because of the slight angle of the engine?
Anyway, the shortened shaft works well with no vibrations or any other issues.