I don't know of anyone who has actually done any testing on the 5S crank to prove that it is weaker.
While they did add two balance shafts to the 5S engine later on (1995 or 1996) that is not related to weakness/longevity issues - it's a NVH issue that manufacturers always talk about.
If you use the 5S-FE pistons and rods, then fitting the head on would be easy, but I can't say what compression you will end up with - the FE pistons are dish type, whereas the GE pistons are dome type.