You put something back together wrong or something's reversed. There is no way you'd have to adjust anything after a throttle shaft swap. Besides, the difference between the two shafts is so minuscule that if any adjustment were required it would be a small one. The only obvious answer is something is backwards. Remove the air cleaner and look at the throttle plate when the throttle control is set to idle. Now move the throttle control to WOT and look at the throttle plate. What are the differences? Any? I'm guessing the throttle plate is fully open regardless of throttle control setting. If this is the case I'd check the linkage for binding somewhere near the governor. Did you use the correct linkage or are the two reversed (choke and throttle)?
Just trying to throw some ideas out there for you. My parts arrived today. Hopefully I'll get it on this weekend.
and the throttle shaft won't close very much even when throttle lever is set to slow idle.
sorry, I just re-read your post and this popped out at me. I am inclined to believe a linkage is binding somewhere not allowing the throttle plate to close. I'd look closely at the governor.