I think I got too aggressive when I loosen the 17mm bolt holding the front engine bracket to the engine mount. I was changing my timing belt and had to raise the engine high enough so the water pump can clear the frame, and while I was raising the engine and loosening up the bolt, the bolt ended up getting removed.

So now I'm trying to install the bolt back for some weird reason it won't go down all the way (see pics). The bolt turns smoothly in the beginning, but when i reached close to the last few millimeters it just won't turn anymore. I did not want to force it cause I don't want to strip the bolt.
Any ideas what I should do?
I've tried raising the engine slightly while turning the bolt down but i still get stuck close to the end.

 

Remove and inspect the bolt for damage. It sounds like it was partially in when you jacked up the engine. Maybe some threads got mangled

 

You may have to nudge the engine block to get the proper alignment. Worst case [excluding thread mishap] you may have to loosen the other mounting points. Key is loosen and not remove.

Salim

 

I think the problem is the bolt, i see some small damage on the thread.. I took the bolt out and shine a flashlight on the bolt hole, hard to see, but I'm hoping the thread on the engine support is ok and just a replacement bolt is needed.

Anyone have the Part number of that 17mm bolt handy?

Dealer is closed today, I'll call them tomorrow if they have the bolts in stock.

 

I did jack the engine up a bit hoping the holes to get aligned, but to no avail. I'll buy a new bolt and hope that will fix the issuel

 

When I'm having trouble lining up holes sometimes a long tapered steel drift helps.
The tapered shape helps get it into a hole that is out of place, and I can move the fixture around until the pin looks to be straight on.

Like this one:

 

Thanks Maxsteel, I'll try that one.

I'm just pissed at the bad design of fastener for the water pump. Most poeple who worked on replacing timing water pumps on RX have that annoying issue with the water pump stud,. I tried removing it with E8 torx, but the stud is too thin and too soft that the end of the stud got sheard.
I tried stud remover but the stud is so thin and I don't want it break and leave a piece inside the hole (that will be a nightmare to take out).
So, I ended up loosening up the bolt on the front motor mount to raise the engine, but I have to raise it high for the water pump to clear the frame, and ended up unscrewing (not loosening) the engine mount bolt.

 

Hope it's a good one, I don't know who made the ones I have.

There are plenty of impossible to get at fasteners. I feel like the engine team doesn't actually talk to the frame team.
My daughters Subaru has things much more accessible. Heck they even put the oil filter on top of the engine. Awesome.

 

So far it's a Major BIG Win for you.
I'd rather deal with this than a snapped off water pump stud in the block. lol

 

The bolt alignment issue is a 3 dimensional problem. Raising will only change the angle very slight bit. You need to twist the engine block. Which way and how much is the million dollar question. Try a wood dowel to sense which side is tight .. please be careful as you dont want to aggravate the problem.
[Learning .. Do not remove the bolt .. just loosen enough]. The problem you are facing is that the other two anchor points are [I think there are 3 support points (not including the torque ... dog-bone at the top)] preventing or biasing the engine block movement. You may have to loosen them. The rubber mounts always put up a fight.

I have this type of stud puller [not purchased from HD]
https://www.homedepot.com/p/GEARWREN...B&gclsrc=aw.ds
With this tool, I can come-up very close the the seized threads.

Engine and body frame observation is very correct. But I think with the engine certification process, Lexus/Toyota fits the engine in multiple vehicles. So the frame design process gives preference to looks and serviceability gets the back seat. My most painful DIY was replacing the solenoid contact points on GS400 ... where the starter is in the valley of the V. One has to remove all the air/fuel plumbing at the top to get to the starter.

Salim

 

Salim's is a much better design than the one I bought.
This one goes less than half way down on the stud and felt like the bolt was starting to twist and snap off.

 

So my bolt was good, I did not see damage on the thread. I think the thread on the motor support got crossed threaded due to engine bracket not aligned with the mount.
I ended up loaning a thread repair tool from autozone and fixed that threads on the engine support. I was finally able to bolt down the engine bracket.
If I had known about the stud remover that Salim pointed out, i might have tried that instead of loosening the front motor mount and lifting the engine to remove the water pump,.
It was just really concerning to put pressure on that thin stud, cause like what Margate said, easier to deal with the motor mounts that having to remove a broken piece of stud.

Talk about hard to reach fasteners and poor design. That bolt on the bottom bracket of the alternator that has the belt tension adjusting bolt is a BIG pain in the A** to install!
I had to position the locking bolt at the lowest position before installing the alternator, but still there's not enough room to get my hands to align the bolt on to the alternator.

And.. whoever designed the oil filter location (which is a frequent maintenance item) trapped between the exhaust manifold at the top of it and the frame and hard lines below it ought to be shot!

Anyways after all my struggles, I am finally done! and my RX is purring like a kitten.
Next will be the oil pan gasket and the thermostat/ lower radiator hose.. but maybe will do it in a couple weeks.. this TB job tired me out lol.

 

I detest that alternator bracket design. It makes a very simple job so much harder.