I'd replace the small case diff, if you haven't done that already. I haven't heard that the 240 is a weak point in the drive train, and from my research BMW's later 4-cyl transmissions aren't much stronger than the 240.
The 260 (or any 6-cyl transmission) will bolt up, but the engine mounting angle is different for the six-cyl cars. The result is that the transmission will be twisted slightly to the passenger side from what I've heard. I'll bet you could modify the transmission mounts and bend the shifter a bit to make it work, but I'd stick with a fresher 240 or go with a slightly stronger e36 M42 or M44 transmission. I think it's a Getrag G5S?