We need more info in order to offer much help. Does your tractor have a 2sp power shift or creeper gear? Makes a difference in how things fit together inside. Does the shifter still feel the same as before the problem, or does it feel like nothing is happening when you shift in and out? Have you looked at a parts breakdown to see what the inside looks like, or do you even feel comfortable going into the trans? If all the linkage you can see moves as you think it should, try disconnecting the rod from the 3rd/4th lever where it comes up out of the top cover and try shifting the lever with no linkage attached to see what it feels like. It should have very little movement before it starts to engage the synchronizer. If it moves very far back and forth with little or no effort, the top cover will have to come off to locate the problem. The parts book shows another lever attached the the vertical shaft and secured with a nut. Can't tell from the picture if it's splined or square drive, but looks like it acts directly on a pin sticking up from the top of the shift fork. You might want to look at the breakdown before pulling the cover off, should it come to that
