From what I was led to believe the weak points are the needle roller bearings, particularly 2nd and 3rd gear and the C52 and C56 EP turbo box's were fitted with stronger needle roller bearings to cope with the extra torque from the output of the turbo equipped engines. I think the input and output shaft bearings were the same, only the actual gear bearings were changed, although I could be wrong.
When you say 414hp with a C56 and 368hp with a C52, are you referring to EP turbo box's? If your referring to a N/A box, then I'm impressed they've held together with that sort of power and hats off to you guys for proving that hearsay doesn't always ring true.
Personally, I wouldn't see the point in fitting another C series transmission to a 4A-GTE (unless you were planning to swap a 4A bell housing onto a EP turbo C52 or C56) when you can just get an E series box that will bolt straight on and not really have to worry about it too much. Plus like you say, the stock gear ratios in any of the 6 speed box's will not really be suited to an engine with lots of available torque. I suppose it's not so bad if you've got a good source of transmissions and the patience to swap them out, I'm just a bit lazy and prefer to try and not have to do a job more than once.
Didn't the 20v Levin GT fitted with a C160 come with a LSD as standard?