Vibration and noise at 40mph and around 1500rpm, feel like exhaust system, but hard to see before the catalytic, it feel so bad, side and rear mount looks good. Could it be inside the engine or transmission? Dealer told me it was the axle, replaced it myself with aftermarket part, but still.

Noise is best diagnosed by tech ears on the noise, not over the internet. Sorry just to much of guessing game

it could be center bearing, if its going bad it can also cause a vibration, make sure you have sufficient fluid in the diff as well, you can also get a noise and vibration from collapsed motor or trans mounts

It's hard to come up with a solution for this one without actually "feeling" the symptoms. I assume that what you're describing is that you can feel vibration coming from the engine. I suggest that you have the engine mounts checked.

Also, make sure the mount that sits just behind the radiator has rubber in the middle of it where the bolt goes through. On some models, the rubber mount is attached to the frame (which attaches to a bracket on the engine). On other models, the rubber part is attached to the engine (which attaches to a bracket on the frame).

I've seen cases where the mechanic had a bracket on the engine and another bracket on the frame. Instead of the mechanic removing one of the brackets and replacing it with the rubber mount, they would just align the two brackets together and run the bolt through them.

This causes the vibration to be transferred directly from the engine to the frame. This will also put stress on the exhaust pipe causing it to eventually break because the engine is not seated properly. The engine will be tilted slightly to the rear...

I would have the front wheel bearing adjustment checked first as if they are loose the rotor will be rubbing on the pads and the vibration will be wheel wobbling on the loose bearings Unless you replaced the bearings with new ones then they will fail especially if the adjustment was too tight and too much grease was used.

I would want to know where the noise is coming from first.
If you had a cylinder not firing, you should get a check engine light with a trouble code stored in the computer.
It could be something hitting the exhaust pipes, a weak motor mount, or any number of other things.
Does it feel like it involves the fact you are at that speed, or the fact the engine is working very hard ?

Get a friend to open the hood and look at the engine go up or down in the engine compartment when the brakes are firmly applied and switching between reverse and drive. Look for the motor mounts for behavior where tears exist in the rubber.

Without feeling the vibration, it is hard to speculate, but, my experience here is this: you may have a bad rear wheel bearing. It is covered for 5 years/60,000 miles by Toyota

If you don't have to be moving to get the vibration then it has to be either something is not balanced properly (torque converter may be bad, front pulley, engine flywheel cracked) or you have a bad mount, causing the vibration from making the engine or trans contact the car body in a place you can't see.
Hard to pinpoint without feeling it myself. I can say for sure it's not the cam belt, unless there's debris stuck to the inside of the cam gear causing the vibration.

#3 - Under vehicle, passenger side, below seating area, mounted in exhaust pipe in rear of catalytic converter

#4 - Under vehicle, driver side, below seating area, mounted in exhaust pipe in rear of catalytic converter

In either case, it is mounted on the rear side of the Cat.

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It is probably your Motor Mounts. They attach the engine in 4 places to the frame of the car. When the rubber wears out, it will cause excessive veibration.

Take it to your mechanic and tell him to check the motor mounts. For the front and side three mounts, it will probably run about $550 with the parts, im guessing.