I bet you are hitting the interlock pin that keeps the tranny from being shifted into 2 gears at once.� You might need to flip the assembly 180* so it slides out of the way.� Also, watch that the new poppet balls are the same size and fill the radius of the cut outs in the shafts.� I had new replacements in a 'kit' and they were too small.� You want to fill the whole radius for full, solid engagement of shifts.
Here is a clip from Rick Stivers T90 rebuild.
http://www.willystech.com/wt/T90RebuildGuide/T90rebuild.htm"Make sure the shift lever is to the inside of this rail also before installation. Insert poppet ball spring and poppet balls into gearshift control housing on the second and high-speed gears side. Insert the second and high-speed gears shifter rail into the gearshift control housing from the rear. If you have difficulty getting the shaft to go in more than about 3 inches inspect the interlock pin to make sure it is out of the way. By now the interlock pin must fit into the detent notch in the low side rail.
Note: This interlock pin is not like the one on the model 18 transfer-case. If you remove this pin it will allow the transmission to shift into two gears at the same time. This would effectively destroy a T-90. DO NOT REMOVE THE PIN. Slide the second and high-speed gears shifter fork onto the rail. Note: it is easy to put this fork on backwards if you aren't careful. When it is properly installed the fork should fall evenly in the middle of the shift tower. Depress the poppet ball and poppet ball spring, using a blunt shaft and slide the rail in over the poppet ball to the second groove. This is the neutral position."
Brett