Pinto Nick

Wonder whether someone can give me a pointer - I had to replace my box recently - so had a recon heavy duty type 9 with taller 1st gear fitted, coupled to an 1800 Zetec blacktop with pinto clutch.
Within less than 100 miles the box has become noisy when coming off the power in 5th - hand on the stick and it feels "rough" with vibration heavy through the stick, also there's a sensation of the engine "snatching" almost like one of the shafts has excess play on it.
Any ideas as to what this may be? The problem I have is the company who supplied the box are adamant it's not the box causing the noise, but I'm certain it is
Any ideas gratefully accepted!!