It must have been too late for me and my old eyes the pin(s) I was referring too are numbers 12 and 13.
Anyway, as I'm sure you're aware that you are going to at least have to remove the linkage assembly. I'm going to be optimistic and think you won't have to drop the tranny as I'm hopeful your issue is in the rear part of that linkage assembly and nothing dropped in to to the box itself. Don't for get to loosen the fan guard for clearance when you angle the transmission. I just pulled the radiator too but I was removing the transmission and I don't have the right type of starter wrench to comfortably reach the top starter bolt without going in from the front with a long extension. And I didn't feel like waiting a few days for the tool to arrive or drive 50 miles to get one. Plus it is much easier and quicker to remove the raditor and intake manifold bracto top bolts (then you can angle it out of the way) then use a extension than it is to turn that bolt 2 degrees at a shot with a standard wrench or socket. For me anyway. If theres a next time forvthe started I think I'll buyvthr right tool. NAPA carries a real cool looking offset "starter" socket priced less than 10$. By the way I believe that wicked upper starter bolt is easier to reach with the transmission angled. Not much but somewhat easier.
Here's the under belly of one from a 3 door Tracker 4wd 2000cc.
I'm not sure if it's really that different from yours. Hard to tell from those diagrams. Anyway. You see the circled pins which I believe are a likely to have slipped loose from the description of your issue. If so the clunk of the shift mechanism would be softer but you have nothing to compare it too. The compartment to the left below the shift lever is sealed from the gearbox. The one right if anything dislodged unfortunately it would fall into the gearbox.
Now that I look closely that hang down dog ear thing is cast or forged as one piece and very unlikely to have broken off. The pin that holds it to the shaft however...
I think the shift lever would indeed feel loose if one of those pins slipped out. Can you hear or fell the clunk of the linkage rod hitting its stops? Both front to back and side to side (the rod turns about 40 degrees and hit stops as you move the shifter side to side like neutral over to get into first or second). There should be a definite feel and click. In my thoughts you could loose the rear pin (right side in the photo) and still get somewhat of a thunk back and forth but little side to side and if the front pin slipped you would feel much of anything except maybe the fitting at the shafts end tapping against the loose rod and or the case in extreme positions.
I'll be curious as to what you find. Again good luck with it. I love happy endings.
By the way this tracker mechanism is about 2 inches longer than the one from my X-90. They are otherwise identical.