For the plug, I had to grind down the outside edges of the spark plug wrench provided by Honda to even get it to fit down in the head far enough to extract the plug.
The XR400 comes with a nicer plug wrench than the 400EX does, but I'm not sure if it fits any better (If I remember correctly, it does). Other than that - there's no plug removal tricks I know of.
Pivot points - like any other bike or quad, they come poorly lubed from the factory. Common trouble areas are the swingarm pivot bolt - it's easy to remove and lube, but will cause you severe headaches if you let it go too long. I use a good synthetic grease on the needle bearings in the arm, and anti-seize compound on the whole length of the bolt. I usually do this about every 8 or 9 months.
The rear shock linkage pivots are caged needle bearings as well, there are 4 of them if memory serves me correctly. Make sure to take them apart when you are doing the swingarm and grease with a good synthetic lube to keep them in good condition and the suspension operating properly.
On the front control arms - Honda uses spherical bearings instead of the bushings used by most of the quad makers - I lube mine every so often, but taking hits on trees usually does them in before they go bad (on the lower arms). Strangely enough, buying a complete lower arm is cheaper than buying new bearings. So... I just replace lower arms every so often at $35/ea (yep, the whole arm - bearings, seals, ball joint, and all is only $35).
Throttle adjustment -
Honda ships (or at least, they used to) 400EX's and other quads with the throttle adjustment at the thumb throttle housing screwed all the way in - which does not allow the carb to open to full throttle. This needs to be adjusted correctly (much like the clutch adjustment). The problem is that most dealers don't catch this during their PDI.
The throttle adjustment procedure is pretty much common sense stuff for the mechanically inclined - I just pulled the boot of the air cleaner side of the carb and observed when the cable was adjusted to allow full throttle, I then verified that it could close all the way to idle, then verified with the quad running that it would idle properly and wasn't affected by turning the bars lock to lock...
