I don't know that I have heard of the autos having bearing problems. But they have other things that can go wrong. And rebuilding an auto is much more complicated and time consuming than a 5 speed.
You also generally won't get as good of MPG with an auto vs. a manual.
Yes, there is a noticeable reduction with a 3 speed auto over a 4 speed auto or a manual tranny. Your RPMs will run about 800RPMs higher at 70MPH with a 3 speed auto in 3rd vs. a 5 speed in 5th. Of course, you could swap in 4.62 axle gears, in place of your current 5.12s.....but how much work do you really want to go to with this auto swap?
As I said before, if it were me, I'd just rebuild the 5 speed, and enjoy 150K miles of trouble free tranny service.