Were the copper injector seats changed with new ones? Perhaps not (old ones used?) which seems to explain why you were seeing bubbling around the injectors.
Why was "never seize" used anywhere near the injectors? You don't want that stuff near or in the injectors, or use it as a sealer for the copper seats.
When I changed my nozzles the first time, I went with cheap .205's and did the swap myself. I was lucky that it worked out great with no pop testing. When I went to the 1019's I sent my injectors to DBW and had them calibrated as well. Took some time and they work great. Both times I changed the seats with new ones. I did see a little leak which showed up as soot around the injector. Gave that injector a love tap and that leak went away. There was a ticking sound that seemed to be associated with the leak.
It is very important that the seats and the injectors are mated as these can leak and your compression will be thrown for a loop. Using old seats will have imprints from the previous install. The ticking sounds could also be these seats leaking as a leak directly from the cylinder can cause noise.
Could it be as simple as putting a new set of seats and gently "tapping" the injectors into these seats for a proper fit?
The jumping IQ values are a concern as well. Did you try "hammering" the IP to see if you can smooth out the fluctuations in the IQ? There is a used IP for sale for $200 locally, I am not sure about the condition but it could be worth the small investment to see if your current IP is failing.
http://dubberz.com/forum/mk4-parts/alh-injection-pump-200-obo-leather-center-console-$40/
Sounds like we need a local GTG where we can all poke around each others cars and solve all the issues
Maybe we can encourage Owain and Mark to host it at their location? Maybe we can get the Dyno out and the BBQ too.