Two pins
One of the pins shown is cut to length on the pin end and both are cut to length on the other (smooth end). I'll show you how to accurately cut the pin end in a minute but now is the time to cut the shank down. Cut off the shank just above the threaded portion of the bolt leaving a bit of the shoulder as shown. The shoulder will provide a positive stop when you thread the pin into the hole in the shift tower. Now cut a slot into the top of the pin so you can use a screw driver to run it into its hole.
Also, the shoulder portion is small enough that it can be recessed into the hole in the shift tower by counter boring with an oversize drill bit. I used a 1/2 bit for this. I counter bored "free hand" with a cordless drill but I don't recommend it. The counter bore depth wont be accurate. That's not really a big deal but the pins will be different lengths and not interchangeable from side to side on the shift tower.
For the counter bore, find a piece of pipe or tube that just fits over the drill bit. A 9/16 ID tube will work well slipped over a 1/2 inch bit. Cut the pipe or tube so that the drill bit (after it is inserted in the drill) only protrudes the amount that you want to recess the pin. Drill your counter bore with the tube over the bit and the tube will cause the bit to stop at the depth you selected. Apologies for lack of pics here.
So far our holes are drilled, tapped and counter bored, the pins have been turned down to an appropriate diameter, the shank has been cut off and slotted. But the pin end still needs cut and they need to be cut accurately.