1993 Camry automatic transmission trouble

[goog1986]

Last week, I took my car (1993 Camry 4 cylinders) to get at my job and when I put it in Drive, I heard a loud knocking sound coming from under the hood. Immediatly, I put the car back in neutral. I try again, and still a huge knock when I put it in Drive, but NOT in reverse! Anyway, I decide to take it around the block. Nothing is goign well, my transmission seems to be shifting right on the 3rd gear so I don't have any power whatsoever...
Anyway, I call my uncle who works at a Toyota dealership and we have a look at it. We realize that my engine mounts are worned out and needs to be replaced. So we change the front one and the upper one (on the passenger side).
The knocking is still present, but is "muffled"... We take the car on a test drive, and still no power when put on Drive! Since the weather is really cold (I live in Montreal) we realize that the transmission is running better and better when it gets hotter. But, when it goes in overdrive, we still feel the knocking! But, if we disable the overdrive, the engine/transmission doesn't knock anymore.
But, still the car isn't changing gears like it should be... He shift into 2nd at 1800rpm and in 3rd at 3000rpm! Usually, it was shifting at around 2500rpm on a normal acceleration.
I did a transmission fluid flush (at a garage) lately and my car wasn't having that trouble usually in winter...
Anyway, I know my thread is long, but can you please help me! Is my transmission good for garbage? or could it be an electrical problem? why is my overdrive knocking?