The rod from the choke to the throttle is part of the fast idle system. When the choke butterfly is closed, the rod operates a bracket surrounding the throttle shaft, which rotates against the throttle positioner screw, opening the throttle and thus providing for a faster idle while the the choke plate is closed. Assuming you have a complete everything correct carb, this rod will not interfer with the choke closing.

Jon.

Good carburetion is fuelish hot air
The most expensive carburetor is the wrong one you attempt to modify.
If you truly believe "one size fits all," try walking a mile in your spouse's shoes!
The Carburetor Shop