Wayne Shamrock vs Masakatsu Funaki - Pancrase: Yes, We are Hybrid Wrestlers 1 (9/21/93)
Wayne Shamrock vs Masakatsu Funaki II - Pancrase: Road to the Championship 4 (9/1/94)
Wayne Shamrock vs Masakatsu Funaki III - Pancrase: King of Pancrase Tournament (12/17/94)
Awesome. I love prime Shammy fights. 
There is a strong possibility the second fight was predetermined because Ken was going to fight at UFC 3 in a week and Pancrase wanted to protect their brand in case Ken lost. 
looking at kens anaconda attempt early in fight 3, the attempt was so bad and so loose, i think he was giving funaki the top position
The first fight between Shamrock and Funaki was the first time Shamrock ever beat Funaki. They fought and grappled for real in training all the time and Funaki always won. That fight was a passing of the torch from teacher Funaki to his student Ken.
However, there is a theory that Funaki let Shamrock beat him so that Shamrock would be launched into an even bigger star for Pancrase. Funaki was the biggest star around and a win over him put you into a rare category.
For the record, I think Shamrock won legitimately.