I also have a 6spd manual bf which had the same clunk, took it to ford and they replaced what they called a "Ball Joint" in the rear end, but still the clunking continued. This clunk wasnt just occuring when changing gears but when going over bumps, and in the wet if I got it spinning it sounded like the rear right wheel was repeatedly bouncing off the ground... TERRIBLE SOUND. Anyway this weekend I noticed that under hard acceleration the car would pull excessively to the side making it a bit of a handful, so I decided to jack it up and take a look myself. when I took the rear right wheel off I grabbed the rotor and could move it forward and backward with little effort, knocking as I done it . What the cause of this all was one of the bolts which obviously holds part of the IRS assembly was LOOSE so I tightened it up and the clunk has now dissapeared haha. how the hell did ford miss this??? Anyways all fix now As for the 1st to 2nd change it is a little notchy sometimes when cold, but if changed at the right rev it just falls into place. Iv found the box is fairly particular with revs but tends to ease up once it gets some heat into it, Dead strong box though