Seems the first dealer should have discovered the issue? Fuel Filters are not specific to just Adventure bikes.
Anyhow, I owned 1 KTM and I have been cured of ever wanting to own another. Maybe a ride or two, but not to own. Too finicky for my tastes.
You liked the KLR and you might want to go back to that but have you thought of picking up a Honda CB500X? What about trading in the 990 for a CB5X and taking the cash difference for alittle MX trip? maybe the dealer in Katy is sympathetic to your plight and will give you a good deal?
There is always a way to make it work. Keep the dream alive.