The new gearbox is a vast improvement but on changing from 3rd to 4th and vice versa there is a grinding sound

The scrap yard that sold me the gearbox assured me that the gearbox was noise free and smooth. 1st and 2nd are fantastic, 3rd and 4th there is a noise when changing.
I'm starting to think that the garage that fitted the gearbox didn't really take to much time with adjusting etc. A quick fit, take out for a test drive, works so-so and that was it sort of thing!
There is no way that that small local garage will take the time to fiddle about with it on the off-chance that it is wrongly aligned linkage because they are more interested in their MOT cash-cows!
My question is do you think this crunching may be caused by incorrectly aligned gear linkage - I read a minute ago on here:
Re: Renewing gear selector fork bushes - advice requested!
by Pootle
“how about I twist the front selector shaft ONE spline anticlockwise in the UJ so the rear shaft rotates slightly further clockwise when I engage first?” anyway what he did worked.
Should I do the same and rotate linkage? I don't really want to start taking gear levers out etc
On the defence of the scrap yard -I think if the gearbox I have was knackered then I would have heard/felt that in 1st and 2nd gear. They are positive that it was smooth etc.
Any advice would help.