[Lancee]

Try cleaning the MAF sensor, there's a decent aerosol cleaner on e-bay for less than £10.

Perhaps try a diesel purge, some people think it's "snake oil" but I have used Liqui Moly (search the 'net for results/information) and I would not agree, it should help with the "knock".
I currently have a 163 (an 02 on 166k and it runs really well) and a later 185 D5 V70, and both have benefitted from the above.
Again, Liqui Moly diesel purge available on e-bay around £14.50 for a litre.
Do make up the plastic pipe and filter "device" and purge directly into the pump and injectors for the best cleaning (search the 'net on how to do this).

There you go, two relatively cheap options which could help/solve your issues.

Where did you get your replacement injector ? I gather reconditioned ones are not always that great.

Probably also worth doing an injector leak off test, again, a cheap and cheerful exercise, explained on the internet and in this Forum.

The best way to get the air box lid and air filter to fit properly is to lift up (unclip) or even remove the air box. the rear edge is a bu**er to seat properly.