I had the same problem, I filed quite alot but it still would not sit completely flush. I just filed untill I got bored, then tried to fit it. There was some play, but with both set screws the bracket stopped moving. Fuel tank went on ok, although I did notice all the body panels etc had a very slight gap. After looking at the whole situation, it's because the bracket doesn't fit flush so it lifts the fuel tank, thus creating the gaps.
Mind you it's only 1-2mm. And the Stabilizer went on without a problem. So I deemed it not worthy of removing the fuel tank and fiddling with it.
The more important thing is, the stabilizer saved my ass at least once since I installed it.....:bom_daisy:
Grey Suzuki DL650 ABS K8
SW-M center stand, OEM crash bars, SV racing parts sliders, Scotts stabilizer, DL1000 Seat, ProTaper ATV High, Acerbis Enduro handguards, Oxford Heated Grips, Murphs forkbrace, GIVI D260ST/Euro Shorty with Madstad, RacerATB corrected speedo gauge, Speedstar protectors, Fenda Extenda, Touratech sidestand extender, TomTom Rider 2 on homemade bracket, KLR650 Pegs