Just replaced my 999 left seal (showa) last Saturday there is a good rough guide on utube also worth downloading work shop manual :
http://www.duc.nu/manuals/download/fmd/md.php as there is a slight difference between them
Have to 'make' 3 'special' tools
1 something to compress and hold spring down to expose lock nut for damping tube and rod - I used an exhaust bracket , two bolts and a luggage strap
2 something to protect the new seal as you put it on - i uesd a plastic freezer bag
3something to drive the new seal into it's seat - I used a 43mm plastic plumbing connector with a slot cut in it.
you need to raise the front off the ground I used a abba stand and a heavy duty ratchet strap from a beam in the garage as there is no hole for a headstock stand.
It took me about 2 hours and all went well, worth having a note pad to record how everyting goes or videoing on phone. Filled with 420 ml shell advance 7.5 fork oil (450 if dry empty) (only 200ml of old very dirty oil left- discarded it, the rest was all over the fairing front wheel and brakes !)
I had the same problem as you no one could do it for about 2 weeks.
PS Worth doing gentle landings on the higher wheelies
Give us a shout if you need help