I have a 98 900rr and I'm having problems with the rear brake. I have to apply a huge ammount of pressure to get it to work. I bled the system, same thing, changed the MC, same thing, changed the Caliper, same thing, new pads, same thing. Someone suggested that I sand paper the rotor, ever heard of that? Any suggestions?

 

What is your idea of a "huge amount"?
Keep in mind that the rear brake should not give too much friction, or else it would lock up easily.
When you brake hard, almost all of the weight goes to the front wheel, and the rear wheel has little weight on it and can then lock up easily. Most of the braking force comes from the front tire, not the back.

Someone else wondered about that. I tested their bike and told them it was normal. I don't know exactly what is going on with your bike but thought my answer was a possibility.

EDIT: cross posted https://cbrforum.com/m_12904/mpage_1/key_/tm.htm#12989