It really is a simple process. Since you already replaced the linkage and didn't measure it, here's what I would do.
1. Take out the linkage totally.
2. Adjust your shifter crank as per http://www.hondarebelforum.com/f28/s...ml#post1162593
3. Thread the lock nuts (6mm threads BTW) all the way down.
4. Screw in 1 end of the shift linkage into the shift crank, ONLY 1 turn max, you just want it to catch and not fall out.
5. Screw in the other end of the shift linkage into the shift pedal.
6. Rotate the linkage into both the shifter crank and shift pedal at the same time. Since the crank is forward threads and the pedal is reverse threads, as you rotate the shift rod, it will pull in both ends. Screw them all the way in until they hit the lock nuts.
7. Now slowly turn the rod in the opposite direction until both crank and pedal arm angles are the same as per post 10 previously provided.
8. Lock the nuts on the shift rod in place.
Now, once correctly done, your problems should go away. If you still have problems shifting, please report back. I only ask that if you do have problems, please report if on cold engine, warmed up engine, choke, no choke, etc.