My engine had the same symptoms, and it turned out that it was not only improperly routed vacuum lines, but too rich a mixture condition. My engine ran very poorly when cold, but once warm, it ran perfectly, despite the overly rich condition.
The difficult part of CIS is that everything operates in concert, so the entire system really needs troubleshooting. A change in one thing invariably causes a change in another area. The only exception might be the AAR, as it serves only to route additional air into the system, but of course, that lack of air might cause someone to adjust the mixuture to compensate.
It's neat stuff when it works!
