If your diesel smokes excessively and idles poorly at cold temperatures then either timing, compression, or glow plug system are not within spec. I've driven IDI diesels for 15 years and they only do that when something's not right. Some white/blue smoke is to be expected, along with a lower idle, but the symptoms I experience with the 1.9 head (and what you're describing with your engine) are misfire symptoms.
The D shaped intake ports are a definite improvement, but the valve size is the same as the 1.6 TD head that I was running before -> in fact, I used the same valves when rebuilding the 1.9 head.
I'm pretty sure all 1.6 er's were 8mm, the earily 1.9's had the same 8mm (dual spring) valves and the later 1.9's had the 7mm single spring ones(not sure which years).