Hyundai iLoad Gearbox & Transmission Problems
Hyundai iLoad 2014: Gearbox whine
You took a share of the responsibility when you went to a clutch place and had a non-factory clutch and flywheel fitted. By doing that you opened the door for Hyundai to walk away from the problem. Had the dealer done the work they might well have found the gearbox problem and could possibly have fixed it under warranty. The only thing you can now do is to go to Hyundai and request goodwill assistance to fix the gearbox problem.
Hyundai iLoad 2012: Manual backlash clunk
I've driven quite a few iLoads and none has exhibited the problem you talk about, and we've had no other reports of this issue from other owners, so it could well be something affecting your van alone. I would persist with the dealer and ask for a fix of some description, which could case of adjusting pinion preload, and if you aren't satisfied with your dealer's response take your complaint further up the chain by talking directly to Hyundai.