Hand brake assemblies are the obvious one - no new ones have been available for years now and its the one rare part that'll keep your car off the road.
The intake boot split wouldn't cause a miss fire, it usually throws lean codes. I'd check all your coils are seated correctly and plugged in nice and tightly.
Its supply and demand really - an increasing number of parts are no longer available from BMW so whilst cars are still being used on the road prices will just continue to increase. I paid £150 for my cruise stalk direct from BMW about three years ago.
Try £6,300 for an unpainted bonnet...get...
I did my headlight for the umpteenth time six weeks or so ago but this time i gave them a blast with a can of clear coat from Lidl. They are still spotlessly clear.
General wear in the gearbox can cause various splines, teeth etc to be slightly out of where they need to be to line up, if you can’t get first then select second and can go straight into first then that’s probably it.
E85 M54, get the rubbers seals that go around the fixing bolts as well. Nothing else you can really change whilst is apart. Oil filter housing gasket is a favourite but there is no crossover in what you have to take apart to do it.
Normal temp is right in the middle of the gauge? Can you feel the radiator to see if its evenly warm all over? The top hose should be hot and the bottom will be much cooler as that's the way the water circulates so cooler water is coming out of the bottom.