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Just replaced front and rear engine mounts on a 2003 Pilot. Front is well covered in other threads but there was no information anywhere about doing the rear. Here’s what I learned.
Back Story. I’m a Toyota guy that bought a Pilot off a friend for 500 dollars. Solid body, 285K miles, new tires and alternator, needed a timing belt, tie rods and had a clunky front end. I’m going to use it as a beater and light hauler. Tie rods (inner and outer) led to lower control arms, struts and strut mounts. Timing belt led to right engine mount. It quieted down a lot but still had a solid clunking sound at low speed over bumpy roads. Did the rev engine thing and both front and rear engine mounts looked bad.
Front mount: you can get the mount out the top without unhooking the radiator hose, battery box or taking the mount apart. Just move stuff out of the way and it will come out.

Rear Mount. Major PITA. Seven hours over two days because I was making it up as I went. The big issue is the thru bolt on the mount. The bolt head sits an inch or so from a hose and is practically unreachable where it sits. This is how it went without all the cussing and staring at the ground while trying to figure out what’s next. All directions are relative to the driver’s seat. Left, driver’s side, right, passenger side.

Jack up vehicle in front and put on jack stands. Remove both front tires.
Remove three 14 mm bolts on the bottom of the rear mount. One long, two short bolts. Place jack on engine and the raise engine. You should be able to get an inch and a half or so. That allows the bolt head to clear the obstruction. Disconnecting the right mount may give you some more travel.
To loosen the thru bolt I used 17 mm socket, a flex joint and three ½ inch, long extensions. I also needed an impact wrench and a 24 inch breaker bar. Feed the contraption through the left wheel well past the steering rack toward the bolt. From the top reach down and fit the socket onto the bolt. From the left wheel well loosen the bolt. My impact would not budge it; I used the breaker bar to release the torque and spun the bolt out with the impact.
Climb back on top, reach around back of the engine and work the mount up and roll to the left side toward the steering rack. After it is free from the engine bracket, manipulate it over the bracket and into the right wheel well where it will come out without much problem. Note: You can lower the engine some to get the clearance back to get it over the engine bracket. Note: mount has two rubber flaps/cushions on the sides and a bump stop on the top. There is also a spacer at the engine bracket that the thru bolt passes thru before it goes into the engine bracket. Transfer the flaps and bump stop to new mount and from the right wheel well feed the new mount over the engine bracket to the left side, climb on top and reach down and manipulate mount back into bracket. Insure flaps are still attached.
These next steps took four hours because I was hot, tired and working with one hand and could not see what I was doing. Hope you have better luck.
Insure engine is raised. Insert long bolt thru spacer, bracket and mount. The new mount should rotate freely on the bolt. Thread long bolt to the point bolt head clears obstruction but mount is still free to rotate. I used a stubby 17 mm gear wrench and it worked like a charm. Lower engine and mount to within ¼ inch of seating on the frame. Start two or all of the 14mm bolts to align mount. Lower engine till mount seats on the frame and takes the weight. Go back on top and tighten thru bolt with stubby wrench as far as you can. This last step was to line up the mount with the frame and limit the amount of preload on the mount (if you had to pry it in place). With thru bolt tightened mount should no longer rotate. Remove 14 mm bolts from underneath and raise engine again to final torque thru bolt (61 Ft lbs.) with daisy chain contraption from left wheel well. Remove daisy chain and lower engine like before to start 14mm bolts and finally seat on frame. Tighten 14 mm bolts, install wheels and that’s it.
Expect to bounce back and forth between the underside of the car and lying on the engine to make small corrections. The hood latch pokes you right in the stomach as you work from the top. I put an old knee pad over it for comfort. Not much room underneath with two jack stands and a floor jack. Good Luck.
 

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Thoses hoses right where your wrenches go - do not get me started about them. Honda scumbags made sure this thing is as hard to maintain as it can get.
 

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My hat is off to you, sir. I've been working on cars since HS auto mechanics class back in 1969. I'm not a professional mech, just the shade tree variety. Done too many repairs to cars that should have just been junked. Removed and replaced too many bolts by feel, because I just couldn't see them. The Pilot is one of the few vehicles that is worth all the extra effort. Thanks for your fine write-up on the rear mount. I've got a new one on the shelf, your post will be helpful when I change it out.
 

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Nice write-up!!! This is definitely the first one I have seen for that rear mount.

And welcome to the forum.
 

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I tried mine this last weekend and failed. I think I have a different engine mount than you used. I have a 2007 2WD. Mechanic I called said they would do for $850. Gulp! Wish someone would video this.
 
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