Knock is when a proportion of the fuel/air mixture self-ignites, rather than burning in a controlled manner as the flame-front progresses through the cylinder. It creates a shock wave and a huge pressure spike that can damage and destroy engines. The 1.8t has knock sensors to detect it, and when it does it will retard the timing and/or reduce boost to protect the engine. The higher the octane, the more resistant a fuel is to knock happening.
The engine does the adjustment on the fly, but i'm pretty sure it also has an element 'long term trim' in regards to knock. I would just run it on 99 for a couple of weeks/tanks and see if the
problem persists before you worry too much. Chances are the fuel in the tank could still be diluted with the lower octane fuel and/or the ECU is still running the timing slightly retarded atm. I know you said the other fuel was 98, but are you 100% sure about that as i'm not aware of a 98 octane being offered in the uk. Any standard fuel is only 95, and even texaco's 'super unleaded' is only 97 octane.
As for mods, it depends on what mods you have done really. Unless it's a big mod then most of the time the engine will adapt fine using the MAF and lambda readings.
The logs can only be run while you are out driving it. They are usually done running WOT from 2000rpm in 3rd gear all the way to the redline. Running them in lower gears is pretty pointless as the car gets through them too quick to see anything useful, and running up to the redline in 4th obviously takes you well into licence losing territory.
Changing the pump is easy, it's accessed from underneath the rear seats and just lifts out once you remove the locking ring. Like i say i'd rule out everything else first though, as chances are it'll be fine and you'll just be wasting your money mate.
