Have recently had to fit a replacement gearbox and clutch to my 97(R) 2000 Turbo due to losing 1st and second gears. Now I get what seems like mechanical vibration/drumming from the rear-end through the first 3 gears under hard power as follow: 1st gear - 2000 to 3500 rpm, 2nd gear 3000 to 4000 rpm, 3rd gear 3500 to 5500 rpm. Have replaced rubber bushes supporting the diff. but no improvement. There doesn't appear to be any backlash in the diff and no play in the universal joint bearings. None of this was happening before the gearbox replacement. Anybody got any ideas?

 

Are any of the "UJ's" got a "notchy" feel when rotated? These do give a good vibration noise even with the slightest feeling of a "tightness" or "flat spot".

 

There are a lot of sheet metal brackets/covers/braces around the box/rear diff, check the bolts used are not touching any moving parts..BUT, I had exactly what you have when I replaced the rear diff cage bushes for powerflex items; the exhaust was JUST touching the rear diff cage close to where the lower suspension arms bolt on. Make sure you have at least a finger knuckle's gap between the exhaust and any part of the body/chassis/suspension.
I eased the fir on mine and instant silence! The exhaust moves a lot when the motor twists on its mountings under accelleration. When all is switch off things seem ok!
Good luck, Graham.