G'day Green62, I spotted a comment on the AF1 forum site recently - the post advised to clean the disc's first to remove any crap that may have built up in one spot. i do this with some Methylated Spirit and paper towel until no more crud soils the towel, but you could use brake cleaner spray (once calipers are removed).
If the dealer has measured the disc for run-out and is sure they are straight, then it could be a number of things in combination.......while you are cleaning disc's you could remove the pads and clean/grease the slider pins and spray wd40 or similar on to the pistons and wipe clean (take care not to spray on brake pads....best to remove them)... I do this at tyre change time and it is really nice to have freshly lubed calipers working properly.
I've had brake shudder before (on my FZR 1000 in 1994) and I had to buy some EBC Braking disc's at great cost back then to solve the issue (the discs were wobbly!).
I doubt very much that the forks could wear out in 19,000kms - I have 30,000kms on my TP and all is well. (I don't do stoppies or wheel stands and ride smoothly, so I rarely need to jam on the brakes unless some moron does the unexpected while I'm having a bad day)......I will replace the fork oil when my front tyre is due, as I think 40,000kms for fork oil is pretty extreme.....
Might be worth a critical look at the front tyre for abnormal wear/front wheel bearings (mine were almost dry when I first checked them at 13,000kms).
Cheers and good luck cleaning!