TODD: If I major in gym, I only have to take four classes my senior year.
LANE: Oh, cool
[Pan to Rory and Dean]
DEAN: We work on our bikes together. He’s got the good tools.
Lane is clearly frustrated by Todd’s apparent lack of intelligence, but their conversation is also making Rory (who has been eavesdropping) doubt Dean’s intellectual capacity. Having Todd as a best friend probably devalues Dean as a boyfriend in Rory’s eyes, despite his excuse that Todd has all the good tools to work on their bikes together.
This comment also reveals that Dean actually does have a motorbike, even though he told Lorelai that he didn’t in Kiss and Tell. Lorelai didn’t believe him, showing that she has excellent instincts. If the motorbike is still not in working order, or wasn’t then, he may have convinced himself he was technically telling the truth.