The trick is to try and get it bent where the two straght ends are actually straight (please don't take that as a jab). The only surefire way would be to use a straight edge after the rod is installed through the ram's mounting hole. I'm assuming you have to thread the sled on after running the arm through the ram's mount. If it is possible to do that without bending the rod any, then try this.
First, make sure the pump arm is straight when it is off the gun using a straight edge. Slide it through the ram's mount, turn end out to mount the sled, then slide the sled into place.
Once that end is done, and hopefully the arm hasn't had to be bent at all, screw the pump arm on -with the pump arm guide sitting inside of the pump arm-. After you have the pump arm screwed onto the pump handle, then thread the pump guide rod into the gun.
Kinda arse backwards; but hopefully that would prevent he pump arm from kinking while being installed; and remove at least that variable from being the cause. I have the same pump arm on my Trilly; and it gets into a weird bind when sliding it onto the gun. Fortunately I'm running a full body; and any massaging back into place has been enough to keep the stroke smooth and kink free.
Either way, I hope you get it sorted out. That Trilly of your is pretty slick!