I've been doing lots of reading here on mods & problems, I thought I had it all covered but then came across something else (on the web) I hadn't read before so I thought I'd just quickly list what I think I know so you can hopefully tell me what I don't yet know. So general 990 issues I know about.
Rideability/jerky throttle - she has good smooth throttle response so I think all is ok there.
Water pumps can leak - I'll just have to keep an eye on that.
Clutch slave cylinder can fail - mine looks original still.
Front brakes can seize so service them often (depending on use).
Tank can be a PITA to get back on - maybe mod the rubber bushes and remove the gas strut if it's there.
Keep an eye out for oil leaks on the casing and for the rear shock leaking.
The dealer warned me that 990's like to kill their batteries - any truth that?

The new one (to me) is the coolant overflow catch tank - make sure the vent pipe isn't kinked as that will allow tank to pressurise.

Have I missed anything?

Rich.

Comrade: Perhaps the most important advice is to ride it.

Not just battery but reg/rec also - search Soft 32 Dat 101 here.

Also, don't miss joys of TuneECU.