The thud in reverse sounds like a clutch problem. Some of these Ford boxes had a synchromesh on reverse, so you won't get the traditional grind that would have warned you of clutch drag on a traditional box. Are the gears engaging properly? Is the change stiff at all? Is there any perceptible difference selecting gears with the engine running, and without?
Regardless, the garage who did the work need to have a look at the van, and be given the opportunity to put it right. I would get it back to them without any further delay.
Good luck. Hope you get it sorted.
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