I have a 2005 T2000 that came stock with ultegra 9 speed and 30/42/53 rings. It shifts very nicely and the dérailleur cage would not come close to hitting the 42 ring even though I have the dérailleur lowered to the point that it just barely clears the big ring. I have had to now switch the middle ring to39 teeth as the Shimano 42T is no longer available. Shifting still works fine albeit a tad slower from middle to big ring than it was with the 42, as you would expect.
I'm baffled by your problem, as it sounds like you have a stock setup that for me worked wonderfully.