I've got a USDM 95 Celica with an AU blacktop and transmission, my 2nd gear is gone and i have found a USDM 5 speed transmission locally but the bellhousings are completely different, can i swap the housing off the tranny that's in my car onto the new tranny I've sourced or do i need to get a whole new tranny from AU or JPN?

Depends on the trans but most likely yes it can be swapped. It's hard to say without knowing what you have but assuming they are both C series then they should swap.
Or you could get the trans rebuilt.