tranny will be fine. the locker wont hurt it. Been running mine for years with a 1.6 efi and 2 lockers...
Well there are some options for springs, but most will lift it a 2" or a little more. Regardless, the best thing you could do is get springs that are longer. So i would do a little searching here for yj conversions, RUF, CJ rear conversions to get an idea of what will work for you.
Keep fireing the questions...