Spoolin90GSX

Hey guys, i'm new to civics, but i've been in the import scene for a while. personally i have a 90 eclipse gsx, but my g/f has a 94 civic ex. its an a/t, with like 140k miles on it. engine is perfect in it, but the tranny is acting funny now. bear with me as i know less than nothing about a/t transmissions. when your in the car, and in second and third gear, between maybe 1500 and 2300 rpms it makes a weird clunking sound. this isn't anything close to a TOB sound, more like a heavy thump thump thump. i searched a lot and found a lot of talk about main input shaft bearings and such, but everything i read involved 5 speeds, so i don't know if its something else or not. if any of you guys have had this problem, please help me out and tell me what to expect to pay, or how to fix it.