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Is the narrative (above) the complete story?

1. When trying to unbolt the filter, is there any chance that you accidentally removed the bolt securing the black lever arm with the detent roller on the end of it?

2. No other bolts were removed or other parts were disturbed after dropping the pan?

3. Was the transmission shift lever left in the PARK position the entire time the transmission pan was removed?

4. Did you at any point disconnect the transmission control cable from the transmission or the shifter mechanism?

Dropping the pan to replace the 'filter' (a totally unnecessary operation as the 'filter' is just a screen, not a particulate filter) will have absolutely no effect on the shift linkage or the parking pawl unless something else got disturbed.

DO NOT drive the vehicle with the parking pawl not fully engaging (your "clicking sound") or you may severely damage the transmission.
 

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Ah, OK, now the full story. The fact that you disassembled the console shifter and played with the shift cable changes everything. There is likely no issue with your transmission, but you've screwed up the detent positions of the shifter vs the detent positions of the transmission.

Somehow you changed the shift cable tension or shifter box detent position relative to the transmission. Depending on how much force you applied, you may have damaged something in the shifter box, but I thinks that's unlikely.

You need to go back and check/adjust the mechanical detents in the shifter box so they are perfectly synchronized with the mechanical detents in the transmission.

1. Disconnect the transmission shift cable from the transmission shift lever.

2. Place the transmission shift lever AND the console shifter in the NEUTRAL position:
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3. After setting both transmission shift lever and the console shifter in the NEUTRAL position, the stud on the end of the shift cable must be perfectly aligned with the hole in the transmission shift lever.

If it is not aligned, you'll need to go back and see what was incorrectly assembled or bent.

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Okay phew! I’m glad to know it’s adjustable. I probably pulled it out of correct tension when I pushed on the shift stick too hard. I’ll do exactly as you mentioned and see if I can get everything back into correct positioning.
Thanks so much
Looking closely at the FSM, I don't see that there is an actual 'adjustment' point (threaded sleeve, etc.) for tweaking cable length.

It seems that this is a 'no-adjustment' linkage, with the cable length being precisely manufactured to the exact length required to match the console shifter detent positions and the transmission detent positions.

Go back and look at everything you touched that's associated with the console shifter and how the cable is attached to it. Make sure the little spring-steel 'U-clip' retainers are positioned correctly.

No adjustment points visible on shifter or cable:
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All I can suggest is that you go back and look very carefully at everything you touched ... looking for witness marks, etc. that might indicate that something is not back in its original position.

Toyota tries to incorporate poka-yoke (mistake-proof) design features in every component and assembly, so it's not clear what could have gone wrong here except that excessive force broke or bent something. I think the console shift mechanism is almost all plastic.

With the shift cable disconnected from the transmission, does the console shifter have the complete series of clearly-defined detent positions? If you unbolt the shifter and shake it, is there anything rattling around loose inside?
 

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Hey so I figured it out. Just wanted to let you know for future reference.
In the shift console, the post that the shift cable attaches to, is actually adjustable. It’s got a nut on its opposite end, and it’s fitted into a slit that allows it to move foreword and backwards. I must have pushed it to the far rear position when trying to push the stick into park. I loosened the nut, slid the post all the way forward, retightened, and reattached the cable. It’s in the correct position now. There’s actually a hole in the side of the plastic shift console that looks like it’s made for getting to that nut(picture).
Thanks again for all your help though!
And thanks for the update. It's great to be able to 'close' this kind of somewhat unusual failure report by confirming what the true root cause was.
 
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