The Mech's that told you lowering your car will mess up your tranny are retarded. the tranny is failing because it probably wasn't rebuilt very well, kind of a problem with our trannys. being lowerd wont affect it in anyway, wouldn't even be able to bottom out and hit it. And if you got a 5spd manual it would be a new world. lol. car will be much more peppy and won't fail unlike the auto trans, just changing the clutch etc normally. And i'm also guessing that your car could use a seafoam job since it's at that many miles.
btw, if you do change the tranny get an h22 tranny, gears are shorter and you'll be able to get up to speed quicker.
And feel free to ask me questions whenever you want, lol