My 2000 NB started life as an 4 speed automatic (the infamous O1M). At 252,000 miles, that finally gave up the ghost and I had a 5 speed manual put in. Having the 11mm pump with the smaller injector nozzles pretty much made it the equal of the 10mm pump with the stock nozzles for the 5speed.
Now at 297,000 miles, my fuel pump died, and I also had much larger nozzles put in - nice bump in power, but it also smoked quite a bit. (The fuel pump was replaced with another 11mm pump).
The following summer, I took the Beetle to Jeff at Rocketchip, and the first comment he had after I told him what was already there was "Smoke much ?" "Like a train any time I hit the throttle". He slightly customized a Stage 2 tune to reduce smoke on the daily driver range (2000-3000 RPM) , but let it all hang out on the upper end. The result is a pleasant to drive daily driver (that doesn't smoke too bad) that can legitimately pull 5000 RPM + on the top .
Tongandiesel - I think you had some timing issues on why your car smoked so much.