Maybe the ABS has got screwed from lack of fluid.
I refer you to the 900A Workshop Manual Supplement 2005 which has details of the ABS and its maintenance.
Some of the content from p65 on is copied below.
• When bleeding the ABS, make sure there is always enough brake fluid before applying the
brake. Ignoring this precaution could allow air to enter the ABS, considerably lengthening
the bleeding procedure.
• If bleeding is difficult, it may be necessary to let the brake fluid settle for a few hours.
• Repeat the bleeding procedure when the tiny bubbles in the hose have disappeared.
• Final check
1. Check the brake fluid level in the brake master cylinder reservoirs.
2. Check the wheel sensors for proper installation.
Hydraulic unit operation test
The reaction-force pulsating action generated in the brake lever and brake pedal when the
ABS is activated can be tested when the motorcycle is stopped.
The hydraulic unit operation can be tested by the following two methods.
•Hydraulic unit operation test 1:
this test generates the same reaction-force pulsating action that is generated in the brake lever
and brake pedal when the ABS is activated.
•Hydraulic unit operation test 2:
this test checks the function of the ABS after the system was disassembled, adjusted, or serviced
3. Perform hydraulic unit operation test 1 or 2.
4. Delete the malfunction codes.
5. Perform a trial run.
Full details in the manual, downloadable from JBX's site:- https://www.tdm-yamaha.heliohost.org/?page=DOC You need to sign up/in.