On reviewing the manual, there are two cautions regarding installing the shift shaft that may be the source of your problem. One, the shaft must be installed with the detents at the front end of the shaft facing upwards. These detents are what the ball/spring seat into when the shaft moves forward/aft (like into 1st/2nd gear). The shaft can be installed 180 degrees out, but you would not feel the shifter 'lock' into gear.
The second caution seems more probable. When inserting the roll pin holding the shift shaft lever and bushing onto the shift shaft, the roll pin must be driven down flush with the surface of the shift shaft lever. If not driven flush, it can bind on or interfere with the movement of the bushing, possibly preventing the lever from being able to engage all of the three shift forks (3/4, 1/2, 5/rev). There are two roll pins used with the shift shaft. The shorter one (7/8") is used to secure the shift shaft lever/bushing and the longer one (1 1/4") to secure the shift socket in the rear.
Unfortunately, confirmation will require removal and partial disassembly (removal of the front case) to confirm.