Problem Solved. Here's what worked for me.

With the window motor assembly still unbolted, I closed the lift gate and reconnected all the electrical connections. I then carefully used the dash control to lower the lift gate window just an inch or so. A few short taps to the switch. This gave enough play that I could easily align and bolt down the assembly.

 

Old thread I realize. And sorry to be wordy, but this is a bit of an exhaustive endeavor.

I was brought up to be thorough. I lost my father recently, and I think of him frequently as I take on projects where more than one set of hands are helpful. Back in the day I was the small set of hands when his big mitts just couldn't get into a tight area. I'm still thankful for all he taught me on how to use tools and to step back and think of an alternative when something was not working.

Several folks are finally getting around to working on their license plate surround-garnish. The pics posted in this thread are most helpful thanks.

I have part numbers for the rubber gasket that surrounds the garnish-that is called a "Protector, Back" 76825-35020.

The 4 plastic (push in) clips that hold the garnish piece to the hatch will likely be destroyed when you push outwards from the inside of the hatch. Those are "Clip-Back Door" 76817-89101

Small hands are most helpful when you work inside the cargo area reaching into the back hatch 'cavity' to remove a 10mm nut below the lock cylinder. The main culprit is 2 plastic splash shields that keep water away from the window's motor assembly. Got a nephew or other small child around? They might really come in handy here. And you can pass on some knowledge that may help them some day.

2 rods must be removed-a large one that attaches to the latch release, a smaller one that attaches to the lock cylinder. Each has plastic retaining clips that slide over the rod to hold it in place. Needle nose pliers work here to help loosen up the clip, but only a small bit of force is needed.

The hatch latch assembly is held to the hatch body also by two 10 mm nuts, there are tight to get at with a socket, and a 10 mm small handled wrench may be more effective. A side note is that the latch handle also attaches to the rear side of the garnish with 3 extremely short Phillips screws. These may already be stripped or the plastic receptacles they screw into have broken off-do not despair, they do not serve any real purpose. But if the screws are missing you may wish to run a magnet inside the hatch cavity bottom to be sure they have not fallen in there and drive you crazy later rolling around as you make turns.

At times it will be helpful to release four other 10 mm bolts that hold the window regulator arms/motor assembly in place inside the cavity. At other times you may want to but back into place at least 2 of the 4 bolts to hold the mechanism in its normal position for easier access to other connections.

Other threads I have read suggested to never start this job without the rear window already down about 1-2 inches, and I agree with that.

Electrical connections to remove are the one for the license plate lights and another one for the lock cylinder. This is again where small hands are most helpful. A small tip flat screwdriver or pick type of tool helps to push in tabs to release such connections.

Miscellaneous tools I found helpful to have in the cargo area with me were long and normal size needle nose pliers, and one of those small mirrors like a dentist uses inside your mouth.

A helper on the outside of the vehicle is most helpful, in my mind almost a must.

A/ To run for tools so you do not have to crawl in and out through the passenger door repeatedly
and
B/ Exerting pulling pressure on the garnish piece as you pinch in the clips.

then later

C/ Holding the window glass in place or even exerting slight upward pulling when you are ready to reinstall all 4 bolts of the window regulator This will take some pressure off of the spring so it will be easier to line up the bolt holes. This is of course when you are ready to put everything all back together.

Once you have removed the mechanical connections and the electrical connections you can work on the garnish more at your leisure without being cloistered in the cargo area.

An excellent time to replace the paint color to match your body color if that is the route you want to go, or go with extreme contrasting color if that is more to your liking. Some 3rd gen owners favor the garnish/surround piece with "4RUNNER" lettering, some like to remove the chrome, whatever suits your needs.

A good time to go ahead and clean up your light lenses, and replace the bulbs with long life LEDs. A good time to check out the lens gaskets and revitalize them. A good time to lube up the lock cylinder. A good time to lube up the hatch release lever. A good time to tighten up the Phillips screws holding the lock cylinder to the back side of the garnish.

A good time to reinforce all plastic attachment points on the back of the garnish piece with Super Glue or Loctite Power Grab (gluelike in a caulking tube), like for 2 of the clips, and the 3 screw receptacles for the latch if you are still lucky enough to have them not be broken.

A good time to be sure your hatch striker is properly indicating 'open door' (AT THE DASH) when the hatch is open, and properly triggering your cargo area dome light when set to the "Door" position. (That is a another job completely unto itself, but just saying since you have the hatch cavity all opened up for the garnish work anyways....)

I've read where others have used gasket type material or even caulk to replace the rubber gasket piece, not a bad idea necessarily until you have to remove the garnish at some point if the latch breaks. Or you strip out the light screws, just saying...

When you are ready to put the garnish back in place, leave the 4 push in clips off and check your fitment, check the latch to be sure that it releases. Keep in mind that the latch DOES NOT have to be attached to the garnish piece to function properly.

It won't release if you do not have the electrical connection in place for the lock cylinder. It won't release if the door unlock button has not been pressed on the driver or passenger door, or on the key fob. It won't release if you do not have the rods reattached for both the lock cylinder AND the latch. Check it out now, you do not want to button everything back up to find out you re-assembled incorrectly.

I realize I have jumped around a bit, but hope this is a bit more helpful than some posts saying it is all intuitive once you open up the cavity.

If you have any experience inside a driver's door panel you will notice similarities in the rod mechanisms of course. But from there it's unlike any other project taken on, but very rewarding once completed.

I now have Natural White (056 color code) for my spoiler and my license plate surround. Much better in my view than a black spoiler and gray garnish piece. And the rubber gasket piece is intact and tight to the body as it should be, the main reason I started the whole thing.