I have faced same problem.I am building an ultimaker clone and I received bent axis. I have seen lot of video for straightening a shaft but they all requires some special setup like dial gauge, some propane torch or some sophisticated machine. Now when you have only 04-06 rods to look after, you should not go for purchasing those exotic showcase piece of measuring instruments.
So I resolved that I would straighten the rods with my own hands (literally!!) and without any dial gauge to the highest possible resolution of human eyes (Fortunately, I am engineer by the grace of God could detect misalignment with quite good with naked eyes).
You see, there is no end to precision you can achieve however bottom line is - it should just work for you. And this is exactly the purpose of my innovation (??).
You will probably laugh at ridiculously simple method when you see the video which is having unfortunately very high level of background noise but believe me I have straightened all four rods with exact same problem as yours with a sketch pen (for detecting runout), 02 bearing with bearing holders (so that you can rotate the steel rods) , one piece of wood (for pressing the rod downwards after you detected run out), 02 great eye ball with safety spectacle on it and 02 strong hands. Just see the video ( I will try to do version without background noise also) and just let me know if any help is required. That is what community is for - we are band of brothers (psst Sisters also - no gender bias).