Originally Posted by Rob Van Name
Are there any standard set up procedures for adjusting the throttle & transmission cables?

Check out the following link to the Ops & Maint manual on this site;
http://j30.us/files/yanmar-manual.pdf

Read pages 12-15. Most likely your operation lever assembly at the clutch/transmission case needs adjusting or is too worn to be adjusted properly. You might also loosen the throttle cable at the engine end to slightly delay the throttle action.
Good Luck,

AC