well I am looking for a short throw shifter for my 1990 legacy LS Wagon 5 speed, and all I can find are short throw shifters for Impreza and legacy 93 and up, a friend told me that the trannys are the same just the body is different, is this true?

yes, same. there are a few minor differences over the years - like hydraulic clutches were available in 96, and the bellhousing bolt pattern changed in 98, external screw on filter added to AT in 98..etc, but for the most part the transmissions are interchangeable with minor hiccups. the shifter i'd think is rather simple.