By looking at the picture I assume you were trying to hold the rod by the big end and mill out the inside of the fork. With this there is no support and the cutter grabbed the rod and sprung it into the cutter. You need more support near the forked end.
Here's what I would do. Find some way to hold the shaft of the rod. I know it's tapered so here's how to hold it. Draw 2 lines on the tapered shaft as far apart as you can get them. Now using micrometers measure the diameter of the shaft at both lines. Subtract the small diameter from the large diameter and divide the answer by 2. This will be the side opposite (trigonometry term) Now divide this number by the distance of the 2 scribed lines. This will be the hypotenuse. Divide the side opposite by the hypotenuse and this will give you the sine of the angle. There are online trigonometry calculators that you can use. Now that you have the angle take a square piece of stock, aluminum if you have it, and put it in the lathe. With a small boring bar set at the calculated angle bore a tapered hole in the block. Now split the block as close to the center as you can using a bandsaw or slitting saw.
A note here: the block doesn't need to be as long as your layout on the shaft of the rod.
Now clamp the rod into the tapered block and set it vertical by using the side or bottom of the rod (big end) Using a ball nose mill cut the round bosses completely off of the fork. Now turn up a piece of stock the same diameter as the bosses and a little longer than needed. Silver solder this piece to the forks. Using the same tapered block clamp the rod horizontally and drill and ream the holes, or whatever needs to be done. Now cut out the center section of the rod with a bandsaw, hacksaw or whatever. Now stand the rod up vertically again like when you cut the notch for the round stock and mill the excess from the sides and center of the forks. .
If all this seems a little too complicated then just saw the bosses off and using a round file, file the notches for the rod but you will still need to make something up to hold the rod closer to the forked end.
gbritnell