I believe the part you are loking for is called a wellnut. It is rubber with a threded insert that compresses the rubber when a screw is inserted and tightened. The same ones hold your windshield on.
The part number for a 2003 954 is:
90111-KW3-003 NUT (5MM) They are $2.74 each at Ron Ayres the link below will take you there.
Ron Ayers Motorsports
Click on the OEM Parts link then on Online Microfiche.
Then at the top of the page click on "Motorcycle" under the Honda Logo
Click on the model year then click on the appropriate model motorcycle (CBR900RR)
The part you describe is #21 on the Upper Cowl 2 drawing for a 2003 954.