All of our suggestions depend upon working components (which we would assume is the case, because they are all new/rebuilt).
The most likely issue is the master cylinder, since YOU rebuilt it... no offense intended. With the brake line disconnected does it pump brake fluid? If not then your rebuild is the suspect. Did you hone the cylinder?
'01 660 Raptor, Burgard +2+1 arms, YFZ Shocks, LSR anti-vibe, CTR pipe, jetted, K&N
'01 Polaris Scrambler 400, K&N
'02 Honda 400ex, Big Gun pipe, jetted, K&N, Lonestar +2 A-arms, Lonestar anti-vibe
'04 Suzuki LTZ400
'16 RZR XP4 1000 Turbo