Here's a short list,
Pull the steering head apart and clean and grease the bearings.
Pull all of your electrical connections apart and blow them out, grease with dielectric grease.
There is a good chance that you have got water sitting on top of the little bladders that go under the front brake, clutch, and rear brake reservoir covers. So the obvious there is to pull them apart and see if there is any water sitting there. May not be a bad idea to go ahead and flush those systems out with fresh fluid anyway.
Changing the engine oil may not be a bad Idea either since it probably got water into the engine via the breather system.
Clean out the gas tank thoroughly.
Use one of the those cable lube devices to force some good lubricant down through the throttle cables and manual decompressor cable.
Disassemble the throttle and clean.
Make sure you don't have water sitting inside the handle bar by blowing it out thoroughly.
Pull the wheels and make sure there isn't a bunch of water sitting inside of the wheel seals.
Pull the swing arm and make sure all of that is dry. May not be a bad idea to lube those bearings anyway and put a thin film of grease on the axle to keep it from seizing in the motor.
Pull the controls apart and clean and lubricate the pivots, front brake, clutch, rear brake etc.
Basically, every thing you can think of to pull apart and check for water incursion, and then lubricate.
One thing I have done with both of my husaberg's with the cast swing arms is to find a spot on the bottom of the swing arm just forward of where it is solid, and drill a small hole to allow water to escape. I used a long ty wrap and stuck in through the lower shock mount access hole down the swing arm to get a measurement for where to drill. This has kept the inside of the arm dry, and the lower shock mount bolts from rusting.