T5 transmission questions

[Forddestroyer96]

Hello I’m working on a 2003 mustang v6 3.8 it’s got a t5 Borg Warner trans it’s junk nothing at all forward reverse clutch is working correctly but it sounds like someone dumped rocks in the trans is there anything I need to look for buying a used trans to stick back in it like different input shaft lengths different input shaft styles or can I just swap bellhousing and put a different one in??? Any input greatly appreciated