Well you could drop in a new engine that runs right but I don't think you are looking for that solution.
If I understand the symptoms you have a low idle until the glow plug relay turns off, about 10 seconds after starting the engine, correct?
During that time I watch my alternator gauge, something VW forgot to install stock. I see it shoot up to close to 30 amps at initial start, then it drops to around 15 for a bit then near Zero when that relay goes click. At the same time the volt gauge, yeah I love real data not some stupid led glowing at me, goes from 12 or so to 13.8 once the click is heard.
What that tells me is that the glow plugs, the starting of the car and running the heater at start up demands a bit of juice from the alternator. That shouldn't drag the engine down if you have the RPM set at the recommended spot. Do you know if you are at 850 or 750? Makes a big difference. Thing shakes like crazy at 750. Does the Alternator get hot to the touch at startup? It should be warm but not hot to the touch. If so you may have one that is bad and just has to work too hard to keep up with the demand. 55 amp or better in VW remember.
As to how you have adjusted the throttle and fuel screws I can only say that without a good look and hear of the engine I am not sure all is well with it. Adjusting the throttle is odd in that you turn it counter clockwise to reset it to get better fueling at times, not the other way around. Marking the position of the throttle BEFORE you adjust it is also a good idea, No, it is the only way to be sure you are going the right way and the right amount. One of those splines at a time.
There is another adjustment to the internal pressure of the first stage of the IP that might be affecting all of your woes. The internal pump pressure is regulated by tapping the inside part of the that button on the front of the pump in with a punch. More often than not it goes too far and you have to remove it, and reset it from the beginning. I use the outflow of the fuel at the back of the pump to gauge if the internal pressure is close. If I really want to get it spot on I have a fitting and gauge I use. But at 1000 rpm you should be pumping a liter of fluid out the back. Just use a 2 liter bottle and mark it half way. That gives you plenty of time to shut it all down, drain the container, and tap the button down a bit more.
Hope that helps.