Tim;
The culprit is probably the transmission. I have a 58 Suburban that had the stock 3 speed on the column. I replaced the stock tranny with an SM319 from a 67 C10 that I found on eBay. The placement of the shifting arms on the side of the tranny that the ends of the shift rods attach to are different. I had the exact same issue. Put the new trans and went to hook up the linkage and the shift rods for 4-5 inches too short.
I ended up going to Ace hardware and picking up some 3/8" aluminum rod and some matching cable clamps. I cut the aluminum rod into two 6 inch sections and clamped the pieces onto the ends of the shift rods to bridge the gap to the shift box on the steering column. It looks pretty country and is only a temporary fix, but it works. Eventually I will get someone to weld steel extensions on the ends of the shift rods.
Unfortunately, I am in Kuwait and my truck is in Missouri so I can't send any pictures.