The AFN turbo is a VNT that was controlled by the computer - it isn't going to work without the ECU.
All of the TDIs that directly bolt in to a Mk2 came with an 02A. The transmission that goes with the engine is what you want - it has the right gear ratios and is strong enough to live behind a TDI.
The Rover pump will do 150 HP no problem. No internal modifications are necessary. All that you'll need to do is turn up the fuel screw a bit and possibly adjust the LDA, but you'd need to do those things no matter what.
Nozzles - the numbers represent a hole size. The bigger the number, the more flow capability, at least in theory. Sizing between different vendors aren't entirely consistent in terms of their actual capability. I have HFLOX Warp-7 (.275) nozzles in my engine which are supposed to be rated for about 230 HP.
To mount the LR pump you'll need to take the pump and the bracket to a machine shop and have them enlarge the mounting hole a bit. The Rover pump has a larger snout on it than the AHU/1Z/AFN pumps. Here in Vancouver, Canada (where rent and labour are expensive) I paid about $75 to have that done, it's probably much cheaper where you live. That will allow you to mount the pump to the bracket. You will also want to find an IP pulley and hub from an ALH or other Mk4 engine - you're looking for the type with the two piece pulley. Without that you won't be able to adjust the timing.
Yes, setting the timing is the same as on a 1.6. You use a dial gauge. The Rover 300 TDI pump I used wanted timing set to about 1.45mm, mine was from an EGR-equipped engine. I think the non-EGR one may have a different cam plate.