Looks like we have been down the same road together on our pagodas. I had the same problem. I took off the long linkage arm from my shifter to the trans linkage from below. I noted that a previous owner had drilled a very small hole on the stud that the bushing slides over. There was a tiny cotter pin that was holding the linkage on. Bushing was shot, so that cotter pin was the only thing holding the rod to the shifter. What a great idea I said! So I drilled a hole on the transmission linkage stud as well. Do a search under my name and you will find my post on the procedure. You must drill the holes in exactly the right spot. Do a mock-up before you drill these holes. No room for error.
I do not see anyway you could drill the stud on the bottom of the shifter while mounted in the car. Shifter would have to be removed. On the Trans end, there was enough room to drill the stud after I supported the trans, and removed the trans support plate.
With those cotter pins installed on both ends, you will never be stranded when the bushings go south. Happened many times to other owners.
Let me know if I can help further.
RB6667