Check out offroadsolutions.com according to them the cranks are different. The crank for the manual tranny has a hole milled into it for the pilot bearing for the input shaft on the tranny. but check the wabsite the have a wealth of info on there.
ORS, last I checked, said that "some" cranks didn't have the pilot bushing milling. If they've changed that to say "all", they are wrong. I have been contemplating a 2000 4runner 3.4 that I have access to for a while. It was shipped w/ an auto, but does have the pilot bushing milling.
