I defiantly know what you mean when it comes to training younger horses. I have to do 3 myself, one will be a year in may, the other 2 in april and another 4 in oct? i believe im not sure
but when i started with my stud i just made sure that he understood that i wasnt going to hurt him, i mean if you can get your horse to trust you then your on the right way. Silvera is right, you should get your stud use to noises like be all calm one min then jump and shout waving your arms the next so hes use to unexpected noises.
I also find that if you can run your hands all over his entire body that really helps. Like..for me i touch my horses everywhere. Their back, shoulders, neck, ears. All down their legs, underneath (not trying to be gross) but around his nuts in that general area, so if by chance something happens hes not going to freak out over it. Once your horse is use to that, use a brush to brush everywhere. I also find that if you can run your hands down his legs and such it will be much easier and more convient for you to pick his feet up when your ready =)
Take your time tho, its not going to happen over night. Hopefully this was helpful to you at least, im sorry if i sorta repeated what Silvera said.